For those who have not completed games in the Xenoblade Chronicles series, this page contains spoilers regarding the plot. Discretion is advised.
The events of Xenoblade Chronicles are divided into seventeen chapters. The player is prompted to save the game at the end of each chapter. Chapter titles do not appear in the game, but have been published in Xenoblade: The Complete Guide. These chapters also determine when certain quests become available or expire.
The story of Xenoblade Chronicles starts off by showing the battle between Mechonis and Bionis, two gods fighting for all eternity. They continue to fight until Bionis cuts off Mechonis' left hand, and then both of their swords pierce each other at the same time. Eons later, life flourished on top of these gods, but the battle waged between Mechonis and Bionis would be continued by their progeny, Bionis' Homs and Mechonis' Mechon.
Centuries later in Sword Valley, the Homs army is fighting off a Mechon invasion. The Homs are quickly losing ground and are forced to retreat to Colony 6 where they will put up a last stand. Dunban, the current wielder of the legendary Monado, decides to ignore orders and engages the Mechon forces with Dickson and Mumkhar. Mumkhar runs away and plans to return after Dickson and Dunban have died to collect the Monado; however, he is killed by the Mechon after running into their base. With the Monado, the only weapon that can pierce Mechon armor, Dunban and Dickson are able to push back and destroy all the Mechon, leaving the Homs victorious and earning Dunban the title of "Hero of the Homs". Unfortunately, Dunban was not able to fully control the Monado, and after the battle, he was unable to use his right arm and almost died from his injuries.
One year later, in the present, an 18 year-old weapons developer named Shulk is rummaging near Mechon scraps in the Mechon Wreckage Site to look for materials that would be useful to Colony 9 when he is attacked by a crab-like monster. Reyn, a close friend of his, saves him and the two quickly head back to Colony 9.
Reyn heads off to the Defence Force, as his break has ended and "Square-Tache" (Vangarre, the colonel of the Colony 9 Defence Force) would not be pleased with him if he was late. Shulk returns to the Weapon Development Lab. Dickson greets Shulk upon the young teenager's return, and after the two talk about the Monado for a while, Dickson tells Shulk to go outside and get some fresh air, since he spends too much time in the lab. Shulk agrees, and heads to Outlook Park, a place where he normally goes.
Meanwhile, Fiora is bringing up some food for her older brother, Dunban, to eat. After talking for a while, Dunban tells her to deliver some food to Shulk, since he would like some. When Fiora worries over him, he laughs and tells her that he will be fine. A hesitant Fiora then heads off with some food for Shulk to the lab. Dickson greets her when she goes outside, and he informs her that Shulk is not at the lab. Fiora, surprised, asks where he is, to which Dickson replies "You know where he'll have gone". Laughing, Fiora thanks him and walks off to Outlook Park.
Shulk is sitting on one of the benches underneath a small tree, looking out to the vast land and water below him. Fiora then comes and sits beside him, handing him the small snack that she had made earlier. The two of them talk for a while, before falling debris from above forces them to return to the colony. This is because the Anti-Air Batteries, which destroy the wreckage, do not cover Outlook Park.
The two teenagers return to the lab, where Reyn is waiting for them. He picks up the Monado, and is then swung around by the sword. Fiora tries to avoid the blade, but it slices straight through her and into a machine next to her. However, the Monado does not damage Homs. She gets angry at Shulk and Reyn when the former worries more about a machine than her own safety, and at Reyn for being so reckless. Reyn asks Shulk to go with him to Mag Mell Ruins, since he needs to obtain Ether Cylinders for the only Mobile Artillery unit in Colony 9. It had crashed into a row of houses in the Residential District, and all of the ether had leaked out in the accident. Shulk agrees, and the two head to Tephra Cave.
Fiora greets them at the entrance, smiling as she throws Ether containers at the two of them (they are needed to collect the Ether). Embarrassed, the two allow Fiora to join them as they battle their way through Tephra Cave. After arriving at the Mag Mell Ruins, the three talk briefly before continuing on. After they go outside into a beautiful plain overlooking the whole of Colony 9, the three head to where all of the Ether Cylinders are stored.
After Reyn has collected what he needs, the trio are attacked by two strange machines, although they are not Mechon. After defeating them, a siren sounds. The three rush outside to witness a horde of Mechon attacking from the skies.
The Anti-Air Batteries try to repel the Mechon, but it results in one of them exploding after a Faced Mechon attacks it. Horrified at the attack, the three rush back to try to defend their home. A quick scene is then shown, showing Dunban limping out of his bed while clutching his right arm in pain.
At the Main Entrance, the three are attacked by a Mechon. Fiora rushes inside to Dunban's House to check on her older brother while Shulk and Reyn engage the enemy. After they disable it, Fiora hurries back outside to tell them that she cannot find Dunban. Shulk, knowing where he might have gone, runs to the lab, avoiding all of the Mechon. Reyn and Fiora follow.
At the Military District, the Defence Force are desperately trying to fight off the invasion. Vangarre yells at his retreating troops to continue fighting, but then Metal Face lands behind. He laughs nervously at the Mechon before blasting it with his gun. The weapon does no damage, and Metal Face throws a vehicle at him, blocking off the entrance to the lab.
Shulk, Reyn and Fiora make it to the lab, only to discover that it is blocked off. Reyn swears revenge on the Mechon for all of his allies' deaths. They remember the Mobile Artillery unit in the Residential District, and run off to refuel it. If they use it to blow up the debris, then they can go inside the lab.
At the crossroads, however, they are cut off by a large group of Mechon. Shulk tells Fiora to run through them and refuel the artillery while he and Reyn distract the Mechon. Fiora, at first, refuses, but then agrees and runs off. After a short battle, the decoration from above falls and blocks off the short route to where Fiora is. Reyn is then attacked from behind and is almost eaten by a Mechon. Shulk tries in vain to save his friend, and then Dunban rushes in to save them, Monado in hand. He easily defeats all of the enemies, and then the three set off to find Fiora.
When they reach the Main Entrance, Dunban is suddenly attacked by a violent rush of pain and falls to the ground. The Monado falls a few feet in front of him, stopping halfway along the bridge. He reaches out for it, despite Reyn and Shulk's protests, but then coughs up blood and collapses. A group of Mechon march up to them from the other side, and Shulk rushes forward to grab the Monado. It glows in his hands, and then he sees a vision of a Mechon's laser striking him. He dodges the blow, having seen it, and defeats all of the Mechon with ease. The two other men stand up, and the three defeat the rest of the Mechon with the aid of Shulk's new ability to see the future.
They hurry along the way to the Residential District, stopping when they come face-to-face with Metal Face. As even the Monado cannot damage it, it easily defeats them, and the three fall to the ground defeated and paralyzed. Just as the Faced Mechon is about to deal the finishing blow, it is blasted in the back by a furious Fiora, who is now in the Mobile Artillery unit. Shulk suddenly sees a vision of her being killed, and shouts at her to run away. However, she refuses to listen and continues to attack. Metal Face slices off an arm of the machine, but Fiora continues the assault on it until she is knocked to the ground. Whimpering, she screams as Metal Face kills her.
Shulk, blinded with rage, screams in anger and rushes forward to attack the Mechon. After defeating them, it flies off after noticed that the other Mechon were leaving and leaves the three to deal with their loss of Fiora.
The next day, Shulk is up in Outlook Park, overlooking Colony 9 as he thinks. Reyn soon joins him, and they talk briefly before the scene flashes to when Shulk and Dunban were talking earlier. Dunban had told Shulk that he will not cry, and to "treasure the gift of life that Fiora has given you". Shulk tells Reyn that he wants to pursue Metal Face and destroy it, and Reyn agrees, although he thought that Shulk would try to talk him out of it. They agree to head to Colony 6, since it is the only other colony left and they may have more information on the Mechon. The two head off, and Dunban watches them from his window, promising that he will join them as soon as his arm heals. Dickson smirks at the two, watching from a wall nearby.
A flashback of fourteen years ago is shown. When Shulk was a child, he took part in an expedition with his parents and four other Homs. They were travelling through a snowy region and came to what appeared to be a tower. When they went through the door, the whole tower began to glow blue. Soon after, Dickson found all the Homs dead but noticed that Shulk was still alive and under a stand that held the Monado. He took both of them back to Colony 9.
Shulk and Reyn head off into Tephra Cave, where they discover that one of the doors in the Mag Mell Ruins that was previously closed is now open. They venture into it and soon find some dead Colony 6 travelers dressed in defence armor. Shulk and Reyn return them to Bionis by putting their bodies into a pool of water nearby, while Reyn comments about how strong the monsters must be if they were able to kill them.
The two friends decide to rest, taking shifts to keep a lookout for enemies. While he is sleeping, Shulk has a strange dream and another vision of the future. The dream shows Shulk talking to a silhouette figure that tells Shulk that everyone wants to change the future; the Monado can help Shulk do this, but if Shulk finds the "True Monado", he can do anything with the future. The vision shows Reyn running away from a group of Arachno spiders, and then into a giant area. A giant spider then stabs him through the chest, killing him. Shulk decides to not tell Reyn about it, but continues on with more caution for fear of his friend. However, Reyn is captured by a sticky white substance into the cave above, and Shulk, worried, starts to run after his lost friend. After a frantic sprint through the cave, Shulk finds Reyn shouting for help as the spiders surround him.
The Arachno Queen then climbs down from above, and Shulk's vision is about to come true as Reyn lifts his shield to defend himself. The Monado then glows, and Shulk uses the first new Monado Art, Shield to save his friend. After an intense battle, the Arachno Queen and her minions are defeated. The two go outside of the cave, arriving on Kneecap Hill, and take in the beautiful view that greets them; Mechonis towering in the distance, surrounded by miles of water. Unbeknownst to them a flying Mechon spies on them and reports to a silhouetted Face Mechon.
When the two reach Bionis' Leg and head into Gaur Plain, they see some smoke rising into the air from beside a body of water. They head towards it only to find a broken buggy, which Shulk is confused by since it looks fairly new, so no one would just abandon it. Shulk, after touching the buggy, has a vision showing a young boy being chased by some giant monsters near a small lake.
Shulk and Reyn search around the area until they find a boy on the ground, at the mercy of two giant monsters. Shulk orders him back, and then the two engage the enemies in combat and win. The red-haired boy tells them that his name is Juju. Shulk and Reyn introduce themselves and Juju tells them about their camp, saying that they can stay there as a "thank-you" for saving him. After giving them instructions on how to get to the camp and Shulk fixes the buggy, the three head there.
When Shulk, Reyn and Juju reach the camp, Sharla, his older sister and a trained medic, walks out and scolds Juju for trying to go back to Colony 6 by himself, before hugging him in worry. After the two separate, Juju introduces Sharla to Reyn and Shulk and she tells them her name. After that, Sharla grabs Reyn's chest and demands to know what happened to Gadolt, her future husband, since he has the Defence Force uniform on. Reyn slowly pushes her off, telling her that he has no idea about who she is talking about. Juju tells her that he offered to let them rest for a while, and Sharla uncertainly agrees to the offer.
After wandering around the camp for a while, Shulk and Reyn go to talk to Sharla. She tells them that their small group made up of Homs and Nopon are the the only remaining Colony 6 people. They fled a month ago when the Mechon attacked, and she is horrified to hear that they attacked Colony 9. Sharla tells them that she is a medic within the Defense Force in Colony 6, and that she is the leader of the small group of people in the camp. Her colonel, Otharon, and Gadolt, a soldier with the Defense Force, are still inside Colony 6.
After discovering that Reyn and Shulk were headed towards Colony 6, Juju pleads with them to take him with them. Sharla slaps him, and then scolds him for being so reckless. He shouts at Sharla that they are all too scared to face the Mechon, and that he will do it if no one else will. Reyn tells him off for disrespecting Sharla, telling him that he should listen to her. Sharla mentions that Reyn acts a lot like Gadolt when he called Juju "kid". Juju grumbles that he will make dinner, and then walks off from the group. After the three talk some more, they hear the sound of the buggy driving off.
The trio rush outside, where they discover the buggy missing and Juju as well. Shulk then sees a vision of a giant Mechon killing Juju and Sharla. Reyn notices this, and then tells Sharla that Shulk can see into the future. Sharla refuses to believe him, but joins the two as they look for Juju. Sharla mentions that he would have most likely headed towards Raguel Bridge, which was founded around the time the first settlers of Colony 9 came, since it was the safest way via buggy to get to Colony 6.
The scene then shows Juju angry at his buggy, since he has crashed it at the start of Raguel Bridge. He continues towards Colony 6 on foot, promising to "show them all". Sharla, Reyn and Shulk give chase to find Juju. They come across the crashed buggy at Raguel Bridge. A little walk later and they arrive at Spiral Valley. Juju is there, but a Mechon M71, a Mechon with many tentacles, grabs Juju. Sharla runs towards him to try and save him, but Shulk remembers that this is where Sharla dies in his vision.
A new symbol appears on the Monado as Shulk creates an aura around Sharla. Sharla has an impressive amount of speed with this aura, and can dodge the tentacles popping up from the ground with ease. After a half battle with the Mechon, it retreats to the roof of their battle field. The three climb up and finish the battle. Juju is saved and the four breathe a sigh of relief. However Shulk says that the Mechon they defeated was the wrong one.
But not for long, as another faced Mechon appears above them. Shulk and Reyn are shocked to learn this Mechon can speak.
The faced Mechon, bulky and clunky in appearance captures Juju and tells the three "I'll be waiting in Colony 6. But hurry, I'm getting hungry!". The faced Mechon then flies off to Colony 6 with a kidnapped Juju in tow.
Sharla is so distraught she faints from the stress and later wakes up in the Refugee Camp from a nightmare about Juju's death. Reyn reassures Sharla that with Shulk's and his help, she will get her brother back. Determined, Shulk, Reyn and Sharla walk through the Colony 6 entrance at the upper level of Bionis' Leg. Sharla points out that the front gate to the colony is probably heavily guarded by Mechon soldiers, so just entering directly through the gate would be too dangerous. She then adds that underneath the Colony is an Ether Mine and that they are connected, so their best chance would be to go through the mines.
The three explore the Ether Mine until they run into Otharon. He reveals that Gadolt disappeared after a failed surprise attack with only his rifle left behind. He goes on saying they take the captured Homs to the Central Pit. It is here Shulk has a vision of Otharon shooting the Faced Mechon in a Mobile Artillery, but falling into a lake of Ether in the process. Shulk tries to warn Otharon, but changes his mind at the last moment, convinced Otharon will not believe him. As such, Otharon leaves the group impatiently to go ahead.
Once they get to the base of the mine they are surrounded by Mechon, and their leader, the same Faced Mechon that took Juju, who introduces himself as Xord. Sharla demands to know where Juju and the others are. Xord replies "Juju? If you mean the brat, he's right here!" pointing at a diamond shaped force-field with an unconscious Juju trapped inside. "As for the others... Well... I just couldn't help myself! I ate them all up!"
Meanwhile Otharon sneaks into the chamber and overhears everything Xord just said.
Enraged, Shulk, Reyn and Sharla fight against Xord, but Xord's strength proves overwhelming. Otharon manages to sneak into a Mobile Artillery Unit and fights Xord himself. Shulk, however, realizes that this is the place where Otharon is to die, and quickly thinks of a plan to save him. Otharon, meanwhile, begins to push Xord into an ether river, where he will disintegrate. In dedication to Gadolt, Otharon pushes Xord enough for him to fall in, but the unit begins to fall in as well. In a nick of time, Shulk comes with a mobile crane, which he uses to grab Otharon. Suddenly, though, the unit suffers an explosion that begins to throw Otharon into the river, much to Shulk's dismay. Fortunately, Reyn runs up the crane and grabs Otharon in midair.
After discovering Shulk's power, Otharon apologizes to Shulk for his behavior and thanks him. He then gives Sharla Gadolt's Rifle. With Juju also in hand, the group begins to head back to the Refugee Camp, but while going up in an elevator, a severely weakened Xord suddenly attacks them. The group fights him again, this time defeating him. Just before he dies, he says that he now sees that Shulk is a hope. When Shulk asks what he means, Xord ends up falling down the elevator shaft and exploding.
The group comes outside to around the Bionis' waist where they are suddenly confronted by a now-talking Metal Face and several other Faced Mechon in identical appearance to Xord. Metal Face taunts Shulk about Fiora, and the group attacks him; however, the sheer number is overwhelming.
Even though Dickson and Dunban (nursed fully back to health and with an Anti-Mechon weapon) come to their aid, the Mechon continue suppressing them. Suddenly, a mysterious bird, which Metal Face and Dickson recognize as a Telethia, attacks the Mechon, wiping out most of them and injuring Metal Face. Shulk then hits Metal Face with the Monado, causing a dent in the armor. At the same time, Shulk receives a vision in which he easily defeats Metal Face.
The Mechon then flee, and the Telethia goes also, coming over to a Homs who asks about Shulk and gets good news. Shulk then tells the group about his vision, and Dickson deciphers that the vision takes place on Prison Island, at the Bionis' head where the presumed mythical High Entia are said to live. The group decides to go there next.
To get to Prison Island, Shulk, Reyn, Dunban, Otharon, Sharla, Juju, and Dickson head through Satorl Marsh, a murky yet beautiful land at the Bionis' waist. When they get to a small post, they set up camp, but Shulk cannot sleep as he is too busy thinking about Fiora's death and his vision. Dickson eventually consoles him.
In the morning, the group gets to the end of the marsh, but they have to get certain items for a Nopon and defeat the Satorl Guardian before they are able to pass. After doing so, Otharon and Juju leave to go help out Colony 6, while Dickson heads back also to continue his travels. But as they leave, Dickson mutters something about deceiving the group. After they leave, Shulk asks Dunban to have the Monado for some time, not feeling worthy of its power, but Dunban tells him to keep it. The group continues on to their next point: Makna Forest. Meanwhile, far away on Mechonis, a silhouetted lady works on a Faced Mechon, whom she refers to as Meyneth.
Deep in Makna Forest, a young girl and four soldiers, who appear to be her servants, fight a large Telethia. The soldiers are killed and the girl is depleted of much of her Ether, thus slipping into unconsciousness.
Traveling through Makna Forest, the group finds the girl, and Shulk realizes that she is present in the same vision. The group takes her under a tree, where Sharla deciphers her condition and realizes she needs Water Ether Crystals, which can be found near waterfalls. Dunban realizes there was a waterfall back at the entrance to Makna Forest, so Shulk decides to go back there alone.
Arriving at the waterfall and getting the proper crystals, Shulk is suddenly confronted by the Homs that talked with the Telethia, and who also appeared in Shulk's dream in Tephra Cave. The man reveals himself to be a simple Homs named Alvis, and reveals that Shulk has become famous amongst all Homs. They are suddenly attacked by a small band of Telethia. Shulk cockily tries to defeat them with his normal tactics and visions, but the Telethia seem to know all his moves, and he is knocked down twice. Alvis tells Shulk that Telethia can read people's minds and see all their moves, regardless of whether Shulk has a vision or not. The only way to defeat them is to purge this ability and attack them from there. Alvis goes as far as to pick up the Monado, unlock the symbol, and kill one of the Telethia. He and Shulk then destroy all the Telethia, but Alvis says they were merely Telethia spawn, and the real one was resting after being "wounded by a girl". He then says that the Monado is capable of destroying the fabric of the universe's existence. Shulk asks how he knows so much about the Monado and how he can use it.
Before Alvis can say anything, Reyn appears, looking for Shulk, as Shulk has been away for a while. Shulk explains why, but when he turns around, Alvis has disappeared, causing Reyn to believe he slept on the job and dreamt this guy up, although he and the rest of the group eventually believe him.
Sharla uses the ether crystals, reviving the girl. Shulk puts a hand on her arm to comfort her, causing her to slap him in retaliation. She then introduces herself as Melia, but refuses to say why she is in the forest by herself and in the first place. Despite this, she decides to repay the group for rescuing her by showing them the way to the Bionis' head via Eryth Sea.
To get there, the group has to go to Frontier Village, a city inside a tree where the comical, weird-talking "furballs" called the Nopon live. Strangely, the Nopon refer to Melia as "Bird Lady". When inside, Melia tells the Nopon ruler Chief Dunga to grant them access to Eryth Sea, and then leaves with a somber attitude. Concerned for her thoughts, Shulk goes to talk to her.
Shulk meets up with Melia, who mutters to herself about a thing that escaped from her homeland, and that she needs to destroy. Remembering Alvis mention the wounded Telethia, Shulk confronts her about the topic, and happens to be correct. He also tells her about how he defeated Telethia, and also about his visions, although she does not believe the latter. Shulk and the rest of the group then offer to help her defeat the Telethia, but she rudely declines. Dunga, however, pesters her into it, and as a bonus, he will even send the village's "Heropon" (finest warrior), whom he is preparing at the moment, to aid them.
While at the meeting place, Dunga introduces the Heropon, Riki, to them in an extremely humorous scene. Although the group finds him useless at first sight (he knows little about the "Dinobeast", and expects the group to get his equipment for him), it is later revealed that the only reason Riki is the Heropon is because if he does this quest, he will be forgiven of several debts he owes the community. At least he knows a place where the Telethia could be-a large batch of Ether Crystals deep in Makna Forest, so the group heads there first.
Arriving at the area, the group discovers it in ruin, as Telethia has absorbed so much Ether that the surrounding area falters in stability. As Melia starts pondering about the Monado's abilities, they are suddenly attacked by the Telethia. They manage to weaken it sufficiently, but in the middle of the battle, they discover that the Telethia also has regenerative powers. The group is shocked at this revelation, and Melia practically gives up on the spot, but Shulk reinstates confidence in herself, and she subsequently develops slight feelings for him. After a while, the Telethia absorbs so much energy that it implodes on the spot, making the mission a success.
Back at Frontier Village, the group begins to say goodbye to the forgiven Riki, but Dunga instead has Riki permanently join the group for Prison Island. The group also discovers that Riki is much older than they thought, having a wife named Oka and eleven children. As the group makes preparations, Melia reveals that they will need imperial sanction by the High Entian emperor to get to Prison Island. They get to Eryth Sea via a pod shaped like a bubble that Reyn finds uncomfortable.
Upon reaching Eryth Sea, the group gets their first glimpse at Prison Island, as well as the High Entian capital, Alcamoth, which the group finds extremely spectacular in terms of its technology. They get to the front door of Alcamoth via transporters (which Reyn also finds uncomfortable). When they get there, the group is met with some High Entia guards that call Melia "Lady", to the others' confusion. Melia goes with the guards and tells the others to wait there while she gets them the aid they need. But after she leaves, more guards arrive, arrest the group, and imprison them in a fancy aerial room.
Unaware of the group's arrest, Melia proceeds onward to meet with the Emperor and give the group sanction. As she heads there, she is shown to be watched by three disgusted individuals: her stepmother Yumea, Yumea's servant Tyrea (who always wears a mask), and an adviser, Lorithia. Surprisingly, it is revealed that Melia is actually the daughter of the High Entia emperor, Sorean, and has a brother named Kallian. She tells them of slaying the Telethia, and as a reward Sorean and Kallian make her next in line to the throne instead, much to her own hesitation. She then learns of the group's arrest, dumbfounding her. Kallian explains that, according to a prophecy, the true heir to the Monado (Shulk) will use the sword to destroy the High Entia. Melia says Shulk would never do that, but Sorean has already sent the High Entia's chief adviser, the Divine Seer, to go interrogate them.
In the prison, only Shulk remains convinced that Melia would never betray them. They then meet the Divine Seer, who happens to be Alvis. Alvis finds them not guilty, and allows them to roam around Alcamoth at their own leisure. Shulk tries to ask him about the Monado, but he leaves. With nothing else to do, Riki tries to go find Melia, but instead they decide to help the High Entia Guards with a rescue mission.
While the group is away, Sorean and Kallian prepare to get Melia's inauguration ceremony ready. Yumea, who is Sorean's First Consort and Kallian's birth mother, suggests that the Trial of the Tomb, a ritual not used in centuries due to so many ancestors dying in the tomb, be used for the ceremony. Kallian protests, but Sorean, seeing no other way, agrees, as does Melia. Yumea later tells Tyrea her woes: she has always hated the Homs, believing them to be worthless and filthy, and has a desire to eliminate them from all contact with the High Entia. As Melia has some Homs blood in her (the Second Consort is always a Homs), Yumea desires to assassinate her as well, even ordering Tyrea to kill the group. Kallian sees this take place, but apparently does not hear them, although he notes Tyrea's mask.
Succeeding in their mission, the group comes to their room to see all of the townsfolk gathered outside for what Reyn thinks is a party and Shulk thinks is a ceremony. From a balcony, Sorean announces that Melia, who is wearing a garment that completely covers her body, is the new heir to the throne, much to the group's shock (except Dunban, who had guessed it), and that she will depart for the tomb immediately. After the ceremony ends, Shulk has a vision in which Melia is killed at an altar.
After Shulk tells the group about the vision, the group is confronted by five women dressed just like Tyrea. They attack the group, but the group quickly defeats them. Alvis arrives to help the group a bit late, and Kallian does as well. Alvis believes the women to be part of a supposed-mythical terrorist group called the Bionite Order, who once served the imperial family, but were presumably eradicated for their extremism. After Kallian remembers Yumea's meeting with Tyrea, Shulk tells him about his vision of Melia, who is being dropped off at the heavily booby-trapped tomb by Lorithia. Kallian, due to High Entia law, cannot permit the group from trying to save Melia (despite Reyn's complaints), but Dunban works his way around it by saying they are not under their law due to their Homs citizenship. Alvis takes them to the tomb. At the entrance, Shulk persists about the Monado. Alvis tells him that he is of a long line of Divine Seers, all of which can see the future and use the Monado. However, their visions all happen through a "ritual" as opposed to Shulk's sudden visions; Alvis interprets this as Shulk having greater power than the Seers. Alvis also says that the Monado's power comes from ether, which it can manipulate. Just before they go into the Tomb, Alvis also whispers "The Bionis is stirring".
Melia goes through a genetic analysis after pressing a button to see if she is a royal High Entia, then proceeds on through the Tomb. When the group gets to the same place, Reyn curiously presses the same button and goes through the genetic analysis. As he is a Homs, a trap door initiates underneath the entire group, causing them to fall a long way down into a small pool. Melia, meanwhile, goes through all of the challenges laid in front of her before coming to the burial place of her ancestor, the first emperor of the Antiqua line. There she encounters an artificial intelligence with the mindset of the first emperor, who tells her that he feels "joy" due to the fact she is 80% Homs, and that she is to be the next empress — and likely the last — but that she is the hope of the High Entia, something Sorean and Kallian see as well; all this confuses Melia. Apparently, Melia's ancestors have long searched for a cure to some curse, and only a specific gene sequence — Melia's — will relinquish them from it. After getting his approval, Tyrea suddenly appears and attacks Melia.
The entire group survives the fall, and they verbally attack Reyn for pressing the button. Alvis settles the confidence, saying that they can still reach Melia (though the distance will be longer). Going through the maze of the tomb, they encounter and defeat an Orluga Rufus (here, Reyn starts to complain). They finally come to where a weakened Melia is. Just as they arrive, a large Telethia appears above them, forcing the group to fight them both. After a long and brutal battle, Tyrea ends up getting her mask knocked off (though her face is still not seen) and the Telethia absorbs too much ether. The group ends up in the blast radius, but Alvis uses mystical powers to absorb the explosion. As Shulk thanks Alvis, Tyrea is revealed to have disappeared. Melia, taking off her mask, thanks the group for saving her, and even cuddles a happy Riki in her arms.
Melia goes to her father and brother with Alvis, and they tell what happened. Melia's coronation is then scheduled to a year following Sorean's death. The group, meanwhile, relaxes in their room, but Dunban is curious to why Melia is to be the next ruler instead of Kallian after seeing Tyrea's rejection of the idea. As they ponder it, Shulk is summoned before Sorean. Sorean asks why the group wants to defeat the Mechon, and Shulk tells him. Sorean then tells Shulk that the Mechon invasion is depleting the ether levels in Bionis, and that according to an ancient prophecy, the Monado is the sword that will save the people; he thus grants the group sanction to assault the Mechon. Shulk then asks to go to Prison Island, but Sorean says that an ancient secret that even the imperials do not know completely about is located there, and no one is allowed there in order to avoid negatively disturbing the secret; Shulk reluctantly obliges. Sorean then asks one more thing "as a father"; he asks Shulk to remain Melia's friend forever, which Shulk gladly accepts. Melia is then announced as being next in line to all of Alcamoth. As this happens, Sharla wonders if Melia's true persona is that of the frail girl they met in Makna Forest or the formal princess they know now. Shulk says she is both, although with uncertainty. Meanwhile, Lorithia and Alvis go over a "plan".
One month earlier, Alvis showed Sorean a vision of the future. The vision, connected with Shulk's big vision, has the group fighting Mechon, only for Sorean to die.
On Mechonis in the present day, Vanea meets with an obscured figure that orders a strike on Prison Island. Some Mass-Produced Faces, led by Metal Face, head there immediately. Metal Face starts taunting a smaller silver-faced Mechon - the same one Vanea was working on earlier - along the way. They encounter the High Entia's Anti-Mechon aerial tanks and engage them in combat.
Desiring to see Melia, the group decides to go hang out with her at her humble Imperial Villa. There they meet her, now with her tiny wings fully exposed, and start talking with her. After the group admires the villa's garden, Melia explains to them the marital practice of the imperial family. For some reason, all Emperors are required to have polygamy with two women, one a High Entia - in this case Yumea, who is Kallian's mother - and the other a Homs - in this case Melia's mother, who died years before the events of the game. However, the practice of marrying a Homs has generated controversy among the racist High Entia, so Melia, due to her mixed blood, is forced to wear her full body garments whenever she is in public. Melia then invites the group to a banquet, which they gladly accept. As she leaves to go make preparations, Shulk has a vision similar to the one that Alvis showed Sorean in the latest flashback - and with the same outcome. This horrifies the unexpecting Shulk, who quickly tells this to everyone. They quickly leave to go stop him after also discovering that the Mechon are attacking.
Unfortunately, Sorean has already left to go to Prison Island. There he intends to create a large barrier that will protect Alcamoth and greatly weaken the invading Mechon. However, to do this he must disturb the secret kept inside Prison Island. The barrier is created and works very well. As it is made, the secret is revealed, which is a member of an ancient, long-thought extinct species known as a Giant, who greets Sorean as if he already knows him.
The group finds Kallian, who grimly tells them that Sorean has already departed. Dunban tries to work his way around Kallian again so that they can save Sorean, but faces harsher resistance. Melia promptly gives them sanction.
After the group unlocks the way to get onto Prison Island and defeats one of the oldest creatures on Bionis, the Skyray, they go to the island, where they come to a huge door blocked by a spell. They see a statue, which is said to be what High Entia looked like in their earliest days, but Reyn and Riki (much to the latter's horror) realize that the statue looks a lot like the Telethia. After Melia breaks the seal via another genetic analysis, the group proceeds through the door. But then Shulk sees another vision, in which he is with the Giant Sorean is with right now, and the Giant decides to "let the shackles be released". Shulk tries to tell the group, but they cut him off.
The group goes to the very pinnacle of Prison Island, where Sorean is with the Giant. The Giant reveals himself to be Zanza, the creator of the Monado. Then he asks Shulk if he wants him to unlock the Monado for him so that he can damage face mechon. Shulk agrees and despite Melia's hesitations, frees the Giant. Suddenly, Metal Face comes out of nowhere and launches a trident at Zanza, killing him. Then Metal Face proceeds to explain their use of ether to disintegrate matter to make killing easier. Sorean catches Metal Face off guard and uses his staff to assault him with the islands Anti-Mechon Defence System. Metal Face falls to the ground and Sorean hugs Melia. But to his surprise, Metal Face rises back up and Sorean pushes Melia out of the way right before being killed by Metal Face.
Shulk was angered that Metal Face killed Sorean, but with Zanza's words he has the Monado change its appearance slightly, it becomes significantly more powerful, and becomes known as the Monado II. Shulk lunges forth with all his strength and attacks Face Nemesis, but then he sees the body of a Homs inside. It is revealed that piloting the Faced Mechon was none other than Fiora, who had apparently survived the incident at Colony 9 and had seemingly no recollection of any of them, to Shulk's disappointment. Metal Face and Face Nemesis then fly away leaving the group all shocked.
Before Sorean dies, he says that this was how it was supposed to be, after he dies Melia is now the empress of the High Entia. Alvis talks to what may be the spirit of Zanza, whose corpse has disappeared. He vaguely mentions how he could have "filled in" for Zanza.
In the Audience Chamber, Kallian tells the assembled ministers that Melia will ascend the throne in one year, and until then he shall assume imperial duties as regent. Lorithia proposes a round-table discussion on strategy concerning the Mechon.
Back in Whitewing Palace, Shulk and Reyn tell the others about Fiora. Shulk, troubled that Fiora did not recognize them, leaves to find Dunban. Dunban tells him it is unsettling, but he is happy to know she is still alive and they must help her to remember.
Kallian summons the party to tell them of his plan to form an allied army and asks them to present this plan to the Homs and Nopon, but Shulk requests time to think it over. The party returns to their quarters, where Melia encourages Shulk to go find Fiora, saying she will stay to help assemble the army. Kallian interrupts their departure and asks Melia to go with Shulk, introducing a woman who will serve as Melia's stand-in during her absence. Kallian relays a report that the silver-faced Mechon fled to Galahad Fortress in Sword Valley. Alvis tells them they must travel down Valak Mountain to reach Sword Valley, and he will accompany them as a guide. A short-range pod takes them to Makna Forest, and they soon reach the passage to Valak Mountain.
In Galahad Fortress, Fiora's Mechon is repaired while Lady Meyneth remarks that Zanza is still alive. She ponders why he took the risk of releasing the Monado's restraints. She finds that she is experiencing feelings for Shulk, and decides she must see him again. Metal Face sees her leave, and remembers that she is Dunban's sister.
The party proceeds down Valak Mountain, stopping for a rest in Ose Tower. Alvis explains that the Monado had been locked away there until it was found by the Homs, and that his and Shulk's ability to see the future was acquired by touching the Monado, which can change the future by disrupting the ether upon which their world is based.
Continuing down to the base of the mountain, they are confronted by Fiora inside Face Nemesis. She still does not remember them, and addresses Shulk as "Heir to the Monado", saying she wishes to talk to him. They are interrupted by the arrival of Metal Face, who shoots Fiora and demands the Monado in exchange for Fiora's life. He complies, and Metal Face's chest opens, revealing the pilot to be none other than Mumkhar.
Dunban demands he answer why he attacked Colony 9, to which Mumkhar says is because it was his home. Dunban angrily charges straight for him, but he quickly remote controls Metal Face to aim one of his claws at Fiora's neck, threatening her life if they take another step. He then demands for them to beg, but Melia thinks otherwise, and blast Mumkhar and Metal Face down with a blast of ether, knocking the remote controlling Metal Face out of Mumkhar as well as the Monado, which Shulk takes back. Mumkhar then releases his flame claws and engages the group in battle.
Partway through the fight, a volley of Mass-Produced Faces drop from the sky as well as a giant golden Mechon, and the pilot says that it is the strongest Mechon built, and introduces himself as Egil, the creator of the Faced Mechon, leader of Mechonis, and agent of Meyneth. Shulk then demands he answer why he puts Homs in the Mechon, however Egil brushes him off and leaves with Mumkhar and Fiora.
As the group arrives in Sword Valley, Dickson greets them, bringing anti-Mechon weapons and news of an alliance between the Homs, High Entia, and Nopon. He then departs with Alvis. After travelling through Sword Valley, the party arrives at Galahad Fortress, where they discover that the Mechon are harvesting a special ether and using it as an acid for their weapons to make killing the life on Bionis easier. They fight Mumkhar again, and just as Dunban is about to kill him, Shulk stops him, saying that they were not there to kill him. Dunban relaxes a bit and then Shulk has a vision of Mumkhar lunging at the party and then accidentally killing himself. Shulk, noticing the events from that vision coming to reality, tries to tell Mumkhar to stop, but Mumkhar refuses to listen. Mumkhar then shoots a beam that breaks off a pillar that impales him right through his body and sends him and his Mechon plummeting towards the ocean screaming "No! No! Not like this!".
The group finds Egil and Face Nemesis waiting to fight them. After the fight, Fiora begs Meyneth, who is still controlling Fiora's body, to help Shulk. Meyneth breaks free from Egil's control and attacks him with a strange power that surprises Egil himself. Egil then defeats Face Nemesis and resolves to take away the memory of the new Faces because he claims that their memories make them weaker. As Face Nemesis unleashes her power, much of Galahad Fortress is destroyed in a chain reaction. Fiora falls off the sword of Mechonis, with Shulk diving after her and the rest of the party falling off into the ocean.
Back in Alcamoth, Kallian receives word that Galahad Fortress has collapsed. Dickson says he has an idea where Shulk's party has ended up, and urges Kallian to begin the attack.
Shulk awakes next to the broken Face, quickly removes Fiora from it, and lays her on the ground. Shulk then makes a fire and waits for her to wake up. Shulk attempts to wake her up by giving her water, but due to the fact that she is unconscious she is unable to drink it. Instead, he drinks it and gives the water to her mouth to mouth by kissing Fiora. She wakes up, saying that it was her first kiss. Shulk asks her if she remembers anything to which Fiora responds that she does. They share a warm hug and she asks for some water which Shulk gladly gets for her. They then set off to find the rest.
They reunite with Dunban and the others in a village, where they meet the Machina, the people of Mechonis. Linada, a doctor, takes Fiora to the infirmary to examine her, and Sharla goes with them. Shulk and the others meet with Miqol, the village leader. Miqol tells them Egil is his son, and asks them to kill Egil.
A party of Homs and Nopon arrive in Alcamoth, led by Dickson, Otharon, and Chief Dunga, to hear Kallian's proposal to form an allied force. After Otharon and Dunga agree, Dickson leaves to find Shulk's party, and Kallian asks him to deliver a message.
Back in the Machina village, Miqol tells the party that Lady Meyneth is the creator of Mechonis, and had fought to defend the Machina from the Bionis. She succeeded in stopping the Bionis, but Egil is now blinded by a desire for revenge. After Fiora's body is repaired, Shulk tells Miqol they must return to the Bionis to warn Kallian of Egil's new weapon, but Dickson arrives and says he will deliver the message. As Shulk and the others depart, Miqol tells them to seek help from Egil's sister, Vanea, who is still in the Mechonis.
Meanwhile, Egil contemplates the situation, realizing that Faced Mechon are flawed because the Homs residing in them still retain memories of their past life. He decided to erase their memories completely, and calls for "Face 20814".
The group leaves the village and heads towards the Mechonis capitol, Agniratha, by travelling up Mechonis through Mechonis Field. On the top floor of Mechonis Field they are ambushed by Jade Face, who is revealed to be Gadolt, Sharla's supposedly dead fiance. He does not recognize her, and fires his Mechon's cannon at the party.
Shulk finds himself floating in empty space, and hears Alvis's voice telling him to find "the true Monado". He awakes to find that he and the others have survived. Vanea greets them and tells they they were protected by Lady Meyneth's power. She says she will take them to Agniratha. Meanwhile, the allied forces arrive at Sword Valley and the battle begins.
Upon reaching the Data Centre in Agniratha, Fiora is temporarily taken over by Meyneth, the goddess of the Mechonis and the "other person" from before. Shulk and the others learn that Bionis and Mechonis were once at peace with one another, before the former inexplicably attacked the latter, killing many of the Machina. Understanding Egil's desire for revenge, the group heads for the Meyneth Shrine where Egil is located. Before they can reach it, they are attacked by Gadolt once more, who opens fire on the group. However the group notices that he is missing Sharla on purpose, and realizes that he can still be saved. With some help from the group, Meyneth in control of Fiora once more assists in bringing Gadolt back to his senses by breaking the control Egil has on him. He then tells Sharla that Egil had good in him before, but was consumed by fear, turning him into who he is now. The group heads off to the Meyneth Shrine, but not before Gadolt asks for Reyn to take care of Sharla.
The group reaches the shrine, where Vanea tries to reason with Egil once more, but is unsuccessful. Egil then reveals to Shulk the reason for his attacks: while holding no hostility towards the Bionis lifeforms, he holds hostility towards the Bionis itself, and the beings there serve as its sustenance so it may awaken once again, so by eliminating the lifeforms of Bionis, it will not receive the ether it needs to re-awaken. Shulk and the group engage in combat with Egil, where Shulk successfully impales him through the shoulder. He tries to reason with Egil once more, but he is unmoved, and removes the Monado from his shoulder. After subduing the group with his Face, Yaldabaoth, Egil retreats to the Mechonis Core to merge with the Mechonis. Realizing that Agniratha is about to be destroyed, Shulk and the group attempt to escape. Sharla, seeing that Gadolt is missing, tries to return to find him, but Reyn convinces her that Gadolt will have left. They fail to outrun the explosion and are about to be obliterated, but Gadolt in his Face appears and shields them, sacrificing himself.
The Mechonis fires an energy beam at the Bionis. Kallian realizes that the Mechonis is awakening and orders an immediate retreat.
Shulk's party find themselves falling, but are rescued by Junks, the Machina having been warned by Alvis that they were in danger. Back in the village they discuss the situation and decide to use Junks to reach the Mechonis Core.
Inside Central Factory they decide to first head for the Apocrypha Generator which is restraining the Monado's power. Shulk begins to wonder if he should use the Monado and cannot figure out why his abilities to know what comes next have changed. He falls to the ground in pain, similar to what Dunban went through, and after some encouragement from Reyn, he explains that it was not caused by the Apocrypha but a different kind of power. On the way to the generator, Shulk begins thinking about the connection between the Bionis Monado and the one he holds, and remembers the dream he had about not being there anymore. They destroy the Apocrypha Generator as the Mechonis begins to move, attacking the Bionis.
The party reaches the Mechonis Core and battles Egil. They manage to save the Bionis by stopping Egil. Shulk prepares to finish off Egil, being encouraged by a voice in his head to do so, until Fiora's words and the memories of his journey thus far stop him from carrying out the task. Egil then asks why he held back trying to kill him, saying that doing so would've ended the war with the Homs and the Mechon and saved his world, to which Shulk says he had forgotten all about the tragedies back on Bionis, but he realizes that both of them shared the same pain, and ultimately says he has no reason to kill him. Egil then says that even if Shulk has no reason to kill him, he still has a reason to kill Shulk, and asks if he will resist killing him even if he killed all the beings of Bionis. Shulk replies that he can at least stop his blade, and that he will continue to until both he and Egil see eye-to-eye. Egil then commends Shulk for using the Monado well, but asks him if he believes that he is its true master. He then tells Shulk a story from many years before when the Bionis and Mechonis lived in harmony. He was asked a question by his friend Arglas of what lies beyond the titans, with Egil replying that he does not know, saying that he is only heard Meyneth say endless sea lies beyond, to which Arglas asks what lies beyond the sea. He then expresses his wishes that one day, their descendants will leave the Bionis and Mechonis to explore and discover new worlds, and that the inhabitants of the two worlds continue living in peace for eternity, intriguing Egil and ultimately he wishes for the same. Egil then tells Shulk that the peace between Bionis and Mechonis was disturbed by the presence of the Monado, which permitted the existence of only itself. Arglas took the Monado himself, and in the process, he was possessed and turned into Zanza. He then engaged the Mechonis in battle before finally being sealed by the High Entia on Prison Island. Shulk then asks if one turns into Zanza if they wield the Monado, to which Egil says that the Monado is Zanza himself, and that he inhabits and possesses the bodies of his own creations to continue his existence. However, he notes that Shulk is a different case, seeing how he maintained a sense of self, and deems that Shulk can break the curse of Zanza, and asks Meyneth, who he accepts as his god once more, if that was not precisely their wish. Shulk then tells Egil that while he does not understand the curse, he can at least promise him that Bionis and Mechonis, as well as its people, can live in peace again, to which Egil agrees, and the two prepare to make a truce. However, Shulk is suddenly shot in the back. Everyone then turns around to see that Dickson has shot him, who menacingly says that Shulk should not have done what he did.
Shulk falls and is quickly caught by Egil. Everyone starts asking Dickson why he shot Shulk, to which he replies that he is just doing his job, then proceeds to focus his sights on Egil, who immediately recognizes him as a Giant and "Disciple of Zanza", which Dickson confirms. He then tells everyone to prepare for Zanza's return. Suddenly, Shulk's body starts glowing and rises into the air. Egil quickly acts and tells Zanza that he will not allow his return, and fires a shot from Yaldabaoth's hand, which is absorbed by Shulk and fired back at Egil. Finally, Zanza, the god of the Bionis, is revived from Shulk's body and he proceeds to take the Monado for himself. He then tells everyone not to be surprised about his return, for this event was already set in the passage of fate. He continues, saying that as everything is interconnected, time eventually leads towards the inevitable, for that is the vision of which he, as the Monado, is the origin. He confirms that everything that happened was predetermined ever since he resided in Shulk. Meyneth tells everyone that after her's and Zanza's battle, he grew weak and his soul within the Monado was sealed in Ose Tower, prompting Dunban to ask how this relates to Shulk. Dickson responds by reminding Dunban that Shulk was among the expedition team that was searching for the Monado; he took Shulk from Ose Tower all those years ago to prepare for Zanza's return, and he informs them Shulk was dead from the start, as Zanza took his life and his family's so he could continue his existence. Zanza tells them that Shulk only appeared alive as a result of him becoming his life force until he matured enough to wield the Monado and allow himself to return. Melia then demands an answer as to why Zanza chose Shulk as his vessel, with Zanza simply saying that Shulk being there was enough for him to choose him as a vessel. Dickson then confirms that Shulk's ability to use the Monado, as well as his visions, were all because of Zanza, and that he ultimately led everyone and everything to their predetermined destinies. From the destruction of Colony 9, to the death of Emperor Sorean Antiqua, and the death of Gadolt; all of these events were by the will of Zanza. Zanza then declares that the time for the destruction and recreation of the world is nigh, but he must first eliminate the Mechonis, and the Bionis awakens once more.
Egil engages Zanza in battle, despite protests from Vanea, claiming he is too weakened to fight. He however exclaims he does not care, for he will gladly give up his life to defeat Zanza, for as his existence continues, Bionis nor Mechonis can attain peace. Zanza then reverts the Monado to another form, saying that Egil's decision to fight him will cause him to cease existing by the wrath of his blade. The Monado then appears on the hand of the Bionis, and Zanza easily destroys the Mechonis' sword and bisects Yaldabaoth and the Mechonis head. He then prepares to lay waste to Mechonis, but Meyneth, finally unleashing her Monado, successfully protects it and Shulk and his friends. She then tells Zanza that she understands now that even as the creators of their life forms, their lives are theirs to control, and if he will only permit his own existence, she will fight for them to show the strength of their will to resist the passage of fate he dictates, and she engages him in battle.
In the ensuing fight, Meyneth is easily overpowered by Zanza, who notes that her full strength has significantly dropped from their last conflict. Realizing that Shulk poses importance to both Meyneth and Fiora, Zanza prepares to kill him, but Meyneth quickly flies over to him to protect him. Zanza then tells Meyneth to face him like a god, or bid farewell to her putrid friends before releasing a powerful blast. Meyneth expels herself from Fiora's body and takes the attack to defend Shulk and his friends. She then begs that they create a world with no need for gods before dying, leaving only her Monado, which Zanza takes for himself. He then sinks Prison Island to the bottom of the sea and releases high concentration ether waves, affecting the High Entia in Alcamoth. Back on Mechonis, Vanea runs up to Egil, who apologizes for everything he is done, then begs for her to leave Mechonis, but she refuses unless Egil escapes with them. However, he tells her that he cannot, for he must fulfill Meyneth's final wish, and Vanea accepts his judgement. Before leaving, he tells her that Shulk can be saved, and to not let the last glimmer of hope be extinguished.
The party then leaves Mechonis through Junks, but Zanza intercepts and prepares to destroy them, but Egil uses one of the arms of Mechonis to block the attack and give the party enough time to escape. Zanza angrily asks if Egil ever gives up, to which he replies he will never, and that he shall be judged not in life, but death. He then uses the remaining arm of the Mechonis to punch a hole through the Bionis' chest. In response, Zanza orders Egil to die, before swinging the Monado full force at Mechonis, causing it to glow blue as it prepares to explode. Egil then begs for Shulk that for the sake of both their worlds, he must succeed, then calls Meyneth's name before he and the Mechonis are killed.
With life on the Bionis in chaos, Fiora, Dunban, and the others flee with Shulk's unconscious body. They reach Junks, which escapes the Mechonis. As they pass over the waters separating Mechonis and Bionis, Dickson attacks the group with a horde of Telethia and prepares to finish them off, until he is stopped by Kallian and his Havres squadron. Kallian is informed of Dickson's betrayal, and prepares to fight him. However Dickson calls for Lorithia, a member of the High Entian court, who turns out to be another Disciple. She releases high concentration ether waves from her Havres, turning many High Entia into Telethia to eliminate life on Bionis. Kallian then apologizes to Melia for burdening her, and uses the last of his will to send his Telethia to take out Dickson and Lorithia, allowing the group to escape back to the Colony 6.
Junks lands in Colony 6 with Shulk unconscious in the infirmary. Fiora places a new weapon which she says was made for him by the Machina based on their research on the Monado. As everyone discusses their options, Melia sees Fiora leave and follows her outside the colony, where Fiora confides that her new body's time is limited. A siren sounds and they rush back to Junks, where they learn a swarm of Telethia is approaching. The party reaches the main entrance in time to see the Telethia arrive, led by Dickson.
Shulk again finds himself floating in empty space, and wonders whether his entire life had been pointless. Alvis appears and tells him "you are the only one who can decide that". He explains Zanza's need for a physical host and his reasons for beginning a cycle of destruction and rebirth. Shulk resolves to stop Zanza, and Alvis tells him he knows what he must do. Shulk places a hand on his own chest, and a white light spreads from his hand to envelop him.
At the main entrance, the party fight the Telethia, but soon find themselves surrounded. Shulk arrives just in time, and Dickson sends his own Sureny Telethia in to attack them. When they defeat it, Shulk tells them he could still see the future. Dickson calls for Alvis to join them, revealing him to be another of Zanza's Disciples, who sends another Telethia to attack the party. When the party defeats it, Dickson and Alvis flee, taking the Telethia with them.
The group uses Junks to reach the Bionis' Interior, flying through the wound made by Egil's final attack. When they reach the heart, Lorithia taunts them, especially Melia, by revealing Kallian is still alive after seemingly sacrificing himself in an explosion before he turned into a Telethia. Lorithia fuses with Kallian's Telethia and the party fights and defeats her. Melia then has a vision, where she speaks with Kallian's spirit. She apologizes for failing to protect her people, but Kallian reassures her, telling her that the High Entia's transformation into Telethia was inevitable, and that as long as she was a half-Homs breed, she would not suffer the curse of her people, and that she was the hope of the High Entia, thus he and her father were happy to sacrifice themselves for her. He then explodes along with Lorithia and before leaving, tells Melia she must now live her own life and make her own choices, for that is the hope of the High Entia. But then when Kallian goes, stating she will never forget her brother's words, the rest of group wonders what's she was saying, but Riki fully understands and had heard what Kallian's spirit has said, Melia then hugs Riki. Dickson arrives to tell the party that he is waiting for them at Prison Island.
The party then travels back to Prison Island to fight Dickson. After chasing him throughout Prison Island, and slaying all of the monsters he sets on them, the party finally reaches the top, and encounter him as turns into his true form: a Giant. The party initially struggles and Dickson reveals to Shulk that since Fiora lost Meyneth's Monado, she has little time to live. However, she convinces Shulk that she is fine, and will fight with him until the end. This, along with the encouragement of their friends, allows Shulk and Fiora to unlock the remnants of Zanza's and Meyneth's power and they defeat Dickson, much to his surprise. He reverts back to his Homs form before dying, and the party leaves as he dies from his wounds smoking one last cigar, but not before expressing his proudness of how far Shulk has come.
Meanwhile, in space, Zanza attempts to look into the future, where he sees the Telethia attacking the Homs, the Bionis in a state of stagnation, and finally, Shulk and his friends engaging him in battle. But suddenly, the vision cuts off after that. Zanza then wonders why he cannot see past that point, stating that with both Monados in his possession, he should be connected with the passage of fate. He then realizes that both Dickson and Lorithia have died in their battles against Shulk, and wonders if the Telethia are growing weak if they are continuing to be felled by his creations. He then remembers Meyneth's dying words: wishing for Shulk to create a world with no need for gods. But Zanza scoffs at this wish, saying that no world can exist without a god. He declares that the world belongs to him before imbuing himself in a mass of energy.
The party then finds themselves in what appears to be a simulation of the Solar System. At the end of the simulation, they catch a brief view of the planet Earth before facing Zanza, now a god-like monster representing the Bionis, and wielding his and Meyneth's Monados. He tells Shulk that he planned to use his body as a dwelling place for the next millenium, but thanks to obtaining Meyneth's Monado, he now possesses all he desires, and says that the beings of Bionis are no longer necessary. He thanks Shulk for providing him with a new Monado and that he has been of more use than his Disciples ever were, then offers Shulk a chance to become one himself. Melia calls him out for being arrogant and treating the lives of Bionis as simple playthings, and that he does not know how it feels for her to kill her own people as a result of them transforming into Telethia. Zanza simply says that the Telethia is the true form of a High Entia, and that the Telethia are simply cells from his own body. He says he gave them sentience to have a short existence as High Entia, to which he believes they should be grateful for. He then tells the group that the beings of Bionis exist only to be his vessels and sustenance, and that Bionis is just an accumulation of their corpses and life energy. Dunban then tells him that while Zanza feigns omnipotence, he was still imprisoned on Prison Island, and calls out how limited he is, to which Zanza simply says he was resting in Prison Island. Having been wounded by Mechonis, he let himself be trapped so that he could await the day when a vessel would be born to him, which Shulk immediately recognizes as himself. Zanza then tells Shulk that he planned to use his body to fight Meyneth, then expresses surprise at her easy downfall. He then offers to make Shulk immortal once more; resolute, Shulk angrily rejects the offer, saying that he simply wants to live a normal life in a world without Zanza. He expresses disappointment that Shulk would think this way, saying that he could've kept peace by leaving all matters to him, but believes that the vision of mortals will remain limited. He then says that using one's power to change the world is a right held only by gods. Shulk then asks if that's why Zanza laid waste to Mechonis, which he confirms, saying that the Machina had become insolent under Meyneth's protection. Reyn then asks if he plans on eliminating the Homs next, to which Zanza replies that he is, for they have proven to be a dangerous species. He expresses disappointment, saying that he had longed for friendship, but now believes that granting intelligence to his creations was a mistake, and that a god should not want friendship. Shulk then says that he is wrong, saying that Meyneth wanted to exist with them, that she saw them as her friends, and that he should have accepted that, then tells Zanza that what he wanted was not friends, but worthless slaves and their lives as his sustenance. Zanza ultimately deems that he was wrong to grant free will to his creations, but brushes it off, saying the Telethia will eliminate every being from Bionis, and that once it's done, he will create a new world like he has many times before. Shulk then says that they cannot allow Zanza the right, and that they will stop him.
Partway into the ensuing battle, Zanza tells Shulk and his friends that if they dare oppose the will of a god, then he will obliterate everything with his incomprehensible power, and proceeds to transform into a god-like monstrosity, taking on the form of a Bionis/Mechonis hybrid with Telethia wings. He then tells the group to behold the true form of a united world before the fight continues. Throughout the fight, Shulk has shown to be able to still have visions, and Zanza proceeds to ask how he can till have them even though he no longer has the Monado. Shulk responds by saying that he does not know, only that it comes from the bottom of his heart, and shows him his enemy and the future he must avert and change. Fiora then tells Zanza that even if they can see the future, it is not set, for there are infinite possibilities depending on what path each individual takes, then tells him that he should know of this more than anyone else, for that is how he has existed. Zanza replies by saying that such a right is reserved only for gods. Shulk then asks why they should care, for it is not important whether or not they can see the future to decide their fate; it is a person's will to make a choice and their strength to seize their destiny that matters. He then closes off by saying that their time has come and that their destiny is their own. Suddenly, light erupts from each of his friends' weapons and directs itself to Shulk's Replica Monado. Upon the light dissipating, Shulk gets back on his feet, now wielding the True Monado. Fiora then tells Zanza that he is not the only one that has the right to decide people's fates, for every being has the freedom to choose the path they wish to follow, and that that is the future. Zanza expresses his surprise that Shulk now wields his own Monado, and asks how it is possible, for they are mere mortals. With that, the final battle begins.
Zanza, now severely weakened, asks how was it possible for them to bring him down like that, for the power of a god cannot be overcome. Suddenly, a voice from out of nowhere tells Zanza that this is a result of the providence of the world, for everything is limited by providence, even a god's power, despite how great it may be. Shulk and Zanza recognize the voice as Alvis, and Zanza berates him for disobeying him. Alvis simply says that he is the Monado; he existed at the beginning, and thus he will also proclaim the end, to which Zanza expresses surprise, saying that that is impossible. Alvis then asks Shulk once more if the world belongs to Zanza or if it belongs to him, to which Shulk says that he made that decision long ago. With a mighty cry, Shulk raises the True Monado into the air as it is enveloped by light once more. Once it fades, the True Monado now displays a 神 symbol, which Zanza notices and takes fear of. Shulk then declares that today, they use their power to fell a god and seize their destiny. He then charges at Zanza and swings the True Monado full force at him. The God-Slaying Sword cleanly cuts through Zanza's body and is split in two. Zanza then utters that all that he was is fading, and that the memories of a god's existence, born from the chaos of creation, is vanishing before he is completely destroyed.
After the battle, Alvis appears before Shulk, and shows him a vision of the past, in which Zanza was once a human scientist named Klaus. He and Meyneth performed an experiment that attempted to create a new universe, but accidentally destroyed their universe and caused the two of them to become gods. They then created the universe of Bionis and Mechonis. Needing a physical host, but unwilling to risk their departure for other worlds, Zanza initiated a cycle of destruction and rebirth to keep life on Bionis, creating beings from the ether and destroying them with the Telethia when they threatened to leave. Alvis then tells Shulk that in all truth, Zanza did indeed wish for friendship, but lost his way. Shulk believes that Zanza's future and their future might have been able to exist alongside one another, which Alvis confirms was a possibility, but is long gone now that Zanza was killed by the very god he created. Alvis reveals that he was originally the administrative computer of the space station where the experiment was performed. Alvis then informs Shulk that their world is expiring, and that Shulk, as its new god, must decide the world's fate: let the old world stagnate, or evolve it to the next stage. However, Shulk says that he simply wanted to stop Zanza from having his way, and that he himself cannot be a god.
Reyn then suddenly appears and agrees that Shulk cannot be a god. Everyone else starts appearing before Shulk. Fiora then expresses that none of them want to be gods either, and that even though they may not know the future, they just want to live life as it comes. Reyn notes the everyday life of eating, sleeping, laughing, crying, even arguing, sounds like a fine life. Sharla then says that simply being with those they love is also enough for them. Melia adds that little by little, everyone changes, and that even though they know that no one day will be the same as the last, they will not know what the future holds for them. Riki proceeds to say that it is better not knowing what the future holds, as life seems more fun that way. Fiora then says that the small surprises in life are what make it great, and that since they do not know what will happen, it may give off a sense of worry, but it also gives off a sense of excitement. Dunban then notes that the fact that they're still continuing to evolve is progress in itself, and that they do not need a more dramatic change than that. Shulk agrees with everyone and says that the changes little by little, as every day passes, should be how everyone lives, and that this is their world. Shulk then finds himself back in the Space Memory, and Alvis apologizes for interfering, saying that he recreated his friends' personalities from his consciousness. Shulk then jokingly says to Alvis that it does not seem like he trusts him to make a decision, and that he is supposed to be the god. Alvis apologizes, stating that his reason for doing so was because the world they know now will not remain longer in its current state. He then asks Shulk for his decision for the future of the world. Shulk simply says that he will not be the one to decide, and that the future should be decided by each and every being in the world. Ultimately, Shulk chooses to recreate the universe as a world without gods, and proceeds to toss his True Monado away. As a result, the Bionis falls and a new universe is formed.
Several months later, Colony 9 is shown, slightly redesigned but otherwise completely different, in that Homs, Machina, Nopon, and even High Entia now all live in harmony. The camera goes into first person perspective, where a person walks down the street and is greeting by various people. The person also sees Vangarre, who is somehow alive, chastising his soldiers again. The person then sees Otharon and Dunban going over trade operations with Vanea, who muses that this is what Egil and Meyneth would've wanted. The person, revealed to be Fiora (although the camera is still first person) then asks Dunban if he has seen Shulk; he says that he went with the group somewhere. As she departs, Dunban tries to say something else, but can only say "Good luck", much to Fiora's confusion. Fiora then comes to Outlook Park, where Melia is alone. Fiora asks what she is looking at, but Melia says she was only thinking about what the future holds. She then thanks Fiora and everyone else for giving her a chance at a new life, because otherwise she would not be here. The girls say they are glad to have met each other, finally confirming their mutual friendship.
Fiora then goes down to the beach, where Reyn is fishing on a dock with Riki, Juju, and Sharla supporting him. Everyone except Sharla ends up falling into the sea when the fish breaks free. Riki then protests, and demands Reyn to catch a fish for him to eat. To get Riki to fish, Reyn reminds him that he must get fourteen fish to feed his family, but this backfires when Riki desperately jumps on Reyn to get him to fish, causing them all to fall into the sea again. Fiora then sees Shulk standing alone, and nervously approaching him she sits on the beach with him. At this point, her body is shown, and she is shown to have been restored into her original body, albeit with shorter hair. Fiora wonders what the future holds. Shulk comments that, although he cannot see the future right now, that's fine with him, because then he can imagine the possibilities. He then recalls his final encounter with Alvis, in which Alvis told him that Shulk's world is the perfect world, and that all life in it will walk together hand in hand toward the future. Shulk and Fiora then vow to meet all the people of this world, "and no matter what happens, we'll face our future together". The camera then pans out, revealing that the Bionis has collapsed.