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 original game, but have been published in Xenoblade: The Complete Guide. These chapters also determine when certain quests become available or expire.
Future Connected serves as an "epilogue", taking place one year after the events of the main game.
- 1 Xenoblade Chronicles
- 2 Future Connected
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 is unable to fully control the Monado, and after the battle, his right arm is permanently damaged and he is left bedridden for a year.
One year later, an 18 year-old weapons developer named Shulk is rummaging in Mechon scraps at the Mechon Wreckage Site to look for materials useful to Colony 9 when he is attacked by a crab-like monster. Reyn, a close friend of his, saves him and the two return to Colony 9.
Reyn heads back 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, where he finds Dickson waiting, having just returned from a journey away. The two discuss the Monado's capabilities, both having been researching it, until Dickson tells Shulk to go outside for fresh air. Shulk agrees, and heads up to Outlook Park.
Meanwhile, Fiora brings food for her older brother - Dunban - to eat. Dunban is only just able to feed himself, but remains resolute that if the Mechon attack again he will need to take up the Monado again, much to Fiora's distress. Fiora then sets off to bring food for Shulk to the lab, but is intercepted by Dickson, who informs her that Shulk is not at the lab. Fiora thanks him and walks to Outlook Park.
Fiora finds Shulk sitting on one of the park benches, looking over the land and water below. She gives him a sandwich and the two 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.
Upon returning to the lab, they encounter Reyn just as he picks up the Monado out of curiosity. The blade activates and swings wildly and uncontrollably around the room, scouring several machines and bisecting one before hitting Fiora directly. However, the Monado cannot damage Homs, and deactivates rather than harm her. Fiora is shaken and angry when Shulk expresses worry over damage to the Monado more than potential harm to her, although Shulk brushes this off. Reyn explains that he came to the lab looking for Shulk to ask him to go with him to Mag Mell Ruins 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 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. 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 the Cylinder Hangar.
After Reyn has collected the ether, 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 descending upon Colony 9.
The Anti-Air Batteries shoot at the Mechon, but one is immediately destroyed when a Faced Mechon attacks it. Shulk, Reyn, and Fiora head back to Colony 9 to help. Dunban is shown 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 her home to check on Dunban while Shulk and Reyn engage the enemy. After they disable it, Fiora tells them that she cannot find Dunban. Shulk, knowing that he may have gone to the Monado, runs to the lab with Reyn and Fiora in time to see the the Defence Force are desperately trying to fight off the invasion and losing. Vangarre yells at his retreating troops to continue fighting, but then a new Mechon arrives. He laughs nervously at the Mechon, disturbed by its face, before blasting it with his gun. The weapon does no damage, and Metal Face throws a vehicle at him, blocking the entrance to the lab. Reyn swears revenge on the Mechon for his fellow soldiers' deaths. They remember the Mobile Artillery unit in the Residential District, and run 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 ahead to refuel the artillery while he and Reyn distract the Mechon. Fiora, at first, refuses, but then agrees and escapes. 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 Dunban rushes in to save them, Monado in hand. He easily defeats all of the enemies, and then the three set off after 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 and wield the Monado without pain.
They hurry to the Residential District, stopping when they come face-to-face with the Metal Faced Mechon. As even the Monado cannot damage it, it easily defeats them, and the three are knocked prone. Just as the Metal Face is about to deal the finishing blow, it is blasted in the back by Fiora, piloting 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 forward to shoot Metal Face point black, finally damaging its face - but not killing it. The mobile artillery is knocked backward by the force of the blast, and Metal Face is able to pick it up from the ground, swing it into a building, and then skewer Fiora with its claws, killing her.
Shulk, blinded with rage, screams in anger and rushes forward to attack the Mechon. It defeats them again, but flies off after the other Mechon begin to retreat, leaveing the three to deal with the loss of Fiora.
The next day, Shulk sits again in Outlook Park, overlooking Colony 9 as he thinks. Reyn joins him, and they discuss the attack - Shulk has already spoken to Dunban, who told Shulk that he would not cry, and that Shulk should "treasure the gift of life that Fiora has given [him]". 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 himself to join them as soon as his arm heals. Dickson smirks, watching unseen from a wall nearby.
A flashback from fourteen years ago is shown; as a child, Shulk 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 entered, the whole tower began to glow blue. Soon after, Dickson arrived to find all the Homs dead except for Shulk, asleep under a stand that held the Monado. Dickson took both back to Colony 9.
In the present, Shulk and Reyn head 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 travellers who they deduce to have been traders. 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 to have killed them.
The two decide to rest, taking shifts to keep a lookout for enemies. While sleeping, Shulk has a strange dream and another vision of the future. The dream shows Shulk talking to a silhouetted 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, and then into an open, webbed area. A giant Arachno 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 and pulled into the cave above. After a frantic sprint through the cave, Shulk finds Reyn shouting for help as the spiders surround him.
The Arachno Queen 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 Reyn's life. After an intense battle, the Arachno Queen and her minions are defeated. The two leave 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 smoke rising from beside a body of water. They head towards it only to find a broken buggy, which confuses Shulk as 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 being attacked by two giant monsters. Shulk orders him back, and then he and Reyn engage in combat and win. The 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 return to Colony 6 alone, 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 and demands to know what happened to Gadolt, her fiancé, since he has the Defence Force uniform on. Reyn pushes her off, telling her that he has no idea who she is talking about; Shulk explains that they are from Colony 9, not 6. Juju tells her that he offered to let them rest for a while, and Sharla agrees.
After wandering around the camp, 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 residents. They fled a month ago when the Mechon attacked, and she is horrified to hear that the Mechon have more recently attacked Colony 9. Sharla tells them that she is a medic within the Defence Force in Colony 6, and that she is the leader of the small group in the camp. Her colonel, Otharon, and Gadolt, a soldier with the Defence Force, are still inside Colony 6.
Upon discovering that Reyn and Shulk are headed towards Colony 6, Juju pleads with them to take him with them. Sharla slaps him, and 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 buggy driving off.
The trio rush outside, where they discover the buggy and Juju missing. Shulk sees a vision of a giant Mechon killing Juju and Sharla. Reyn notices this, and tells Sharla that Shulk can see into the future. Sharla refuses to believe it, but joins the two as they look for Juju. Sharla mentions that he would have most likely headed towards Raguel Bridge, since it is the safest way via buggy to get to Colony 6.
The scene then shows Juju, angry, having crashed his buggy at the start of Raguel Bridge. He continues towards Colony 6 on foot, promising to "show them all". Sharla, Reyn and Shulk come across the crashed buggy and shortly 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, lending her an impressive amount of speed to dodge the tentacles emerging from the ground. After a half battle with the Mechon, it retreats to the roof of the valley. The three climb up and finish the battle. Juju is saved and the four breathe a sigh of relief, but Shulk notes that he saw a different Mechon in his vision.
As predicted, another faced Mechon, rounder and more bulky than Metal Face, soon appears above them. Shulk and Reyn are shocked to learn this Mechon can speak, especially as it uses its voice to belittle them; it is far stronger than them and defeats them easily, aiming to kill until the lights on its body change colour from red to green and it takes up Juju and retreats to Colony 6.
Sharla is so distraught she faints from the stress, waking four hours later 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, who reveals that Gadolt disappeared after a failed surprise attack with only his rifle left behind, and that Mechon take the captured Homs to the Central Pit. 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. 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, 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!" 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, realises that this is the place where Otharon is to die, and quickly thinks of a plan to save him. Otharon begins to push Xord into the ether river below, 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. Shulk manages to manoeuvre a mobile crane, which he uses to grab Otharon's vehicle but the unit suffers an explosion throws Otharon into the air. Shulk thinks he has failed, but Reyn runs up the crane and grabs Otharon in mid-air, saving his life.
Otharon apologizes to Shulk for his behaviour and thanks him, recognising his abilities. He then gives Sharla Gadolt's Rifle. With Juju also in hand, the group begins to head back to the Refugee Camp, but while ascending on the elevator, a severely weakened Xord reappears and attacks them. His armour has been corroded by the ether and he is defeated easily. Just before he dies, he mentions that Shulk has yet to unlock the true power of the Monado. When Shulk asks what he means, Xord topples down the elevator shaft and explodes.
The group arrives outside, 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's death, and the group attacks him; however, the sheer number of Mechon is overwhelming. Dickson and Dunban, now well enough to fight with his uninjured hand, arrive as reinforcements but are still surpassed by the Mechon.
Suddenly, a mysterious flying creature, which Dickson recognise as a Telethia, attacks the Mechon, wiping out most of them and injuring Metal Face. Shulk manages to hit Metal Face with the Monado, denting its armour. At the same time, Shulk receives a vision in which he easily defeats Metal Face. The Mechon flee, and the Telethia goes also, landing on a hill beside an unknown 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 decide 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 rebuild Colony 6, while Dickson leaves to continue his travels. As they leave, Dickson mutters something about deceiving the group. After they leave, Shulk asks Dunban's permission to use the Monado, and Dunban tells him to keep it. The group continues on to their next point: Makna Forest. Meanwhile, far away on Mechonis, an unfamiliar silhouetted woman 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, slipping into unconsciousness. The group find her unconscious and ether-deficient, and Shulk realizes that she is present in his vision of defeating Metal Face. He also has a vision of fighting a huge Telethia with her. The group move her to shelter, where Sharla deciphers her condition and realizes she needs Water Ether Crystals, which can be found near waterfalls. Dunban notes there is a waterfall back at the entrance to Makna Forest, so Shulk decides to go there alone.
Arriving at the waterfall, Shulk is confronted by the man seen communicating with the Telethia, who also appeared in Shulk's dream in Tephra Cave. The man reveals himself to be a Homs named Alvis, and that Shulk is "famous amongst all Homs". They are attacked by four small Telethia. Shulk tries to defeat them using visions, but the Telethia know his moves, and he is knocked down twice. Alvis tells Shulk that Telethia can read people's minds, rendering Shulk's visions moot. The only way to defeat them is to purge this ability; Alvis picks up the Monado, unlocks the symbol, and kills one of the Telethia himself, to Shulk's amazement. He and Shulk destroy all the Telethia, but Alvis says they were merely Telethia spawn, and the real problem is resting after being "wounded by a girl". He adds that the Monado is capable of manipulating ether. Shulk asks how he knows so much about the Monado and how he can use it.
Before Alvis answers, Reyn appears, looking for Shulk. When Shulk looks back he finds that Alvis has disappeared, and Reyn assumes Shulk to be making things up. Alvis is revealed to watch them leave from afar. Shulk and Reyn return to the party, and Sharla uses the ether crystals to shoot ether into the air, reviving the girl. Shulk puts a hand on her arm to comfort her, causing her to slap him in retaliation. She introduces herself as Melia, but refuses to say why she is in the forest alone. 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 giant tree where Nopon live. The Nopon refer to Melia as "Bird Lady". When inside, Melia asks the Nopon ruler Chief Dunga to grant them access to Eryth Sea, and then leaves with a sombre 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 that she needs to destroy. Remembering Alvis mention the wounded Telethia, Shulk confronts her about the topic, and is correct. He also tells her about how he defeated Telethia at the lake, 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 declines. Dunga, however, persuades her to agree, and as a bonus, he will even send the village's "Heropon" (finest warrior), whom he is preparing at the moment, to aid them.
At the meeting place Dunga introduces the Heropon, Riki, to the party. Although at first they find him underwhelming (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. He does know 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 almost gives up, but Shulk reinstates her confidence in herself, and she subsequently develops slight feelings for him. Melia is able to bombard the Telethia with so much energy that it implodes, making her 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 technologically spectacular. They travel to the entrance of Alcamoth via transporters (which Reyn also finds uncomfortable). When they get there, the group is met by High Entia guards who address Melia as "Lady", to the others' confusion. Melia goes with the guards and tells the others to wait while she gets 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 to meet with the Emperor and give the group sanction. As she heads there, she is watched by three disgusted individuals: her stepmother Yumea, Yumea's masked servant Tyrea, and an adviser, Lorithia. It is revealed that Melia is actually the daughter of the High Entia emperor, Sorean, and has an older brother named Kallian. She informs them that the Telethia has been slain, and Sorean announces that she will be next in line to the throne. She then learns of the group's arrest; 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 interrogate them.
In the prison, only Shulk remains convinced that Melia would never betray them. They meet the Divine Seer - 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 Melia's inauguration ceremony. 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 its lethality, be used for the ceremony. Kallian protests, but Sorean, recognising the prestige it would bring, agrees, as does Melia. Yumea later conspires with Tyrea: she has always hated 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 Homs blood (the Second Consort is always a Homs), Yumea orders Tyrea to assassinate her in the Tomb. Kallian sees this take place, but does not hear their words, although he notes Tyrea's mask.
After returning to their room having rescued the High Entia worker, the party see High Entia gathered below outside. From a balcony, Sorean announces that Melia, seen wearing a garment that completely covers her body with a ceremonial mask, is the new heir to the throne. Dunban is the only member of the party not surprised by this. Melia is to depart for the trial of the tomb immediately. After the ceremony ends, Shulk has a vision in which Melia is killed at an altar.
After Shulk relays the vision to the others, they are confronted by five assassins dressed like Tyrea. Alvis arrives to help, having foreseen the attack, but arrives after the assassins are defeated. Kallian follows soon after; Alvis believes the assassins to be part of a supposed-mythical terrorist group called the Bionite Order, who once served the imperial family, but were eradicated for their extremism. Kallian recalls Yumea's meeting with Tyrea,and Shulk explains his vision of Melia being assassinated. Kallian, due to High Entia law, cannot permit the group to enter the Tomb (despite Reyn's complaints), but Dunban works his way around it by saying they are not obligated to follow this law due to being Homs. Kallian relents, and Alvis takes them to the tomb. At the entrance, Shulk asks again about the Monado. Alvis reveals himself as part of a long line of Divine Seers with the ability to see the future and use the Monado. However, their visions happen through a "ritual" as opposed to Shulk's sudden visions; Alvis interprets this as Shulk having greater power than the Seers. Just before they enter the Tomb, Alvis also notes "The Bionis is stirring".
Melia enters the tomb via a scan determining her a genetic analysis. When the group reach the same place, Reyn presses the same button and is also analysed - but as a Homs, he is deemed an intruder, and a trap door opens causing the party to fall a long way down into a pool of water. Melia, ahead and alone, fights through the challenges to reach a chamber containing an artificial intelligence with the mindset of the progenitor of her family, 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, which Sorean and Kallian have said; all this confuses Melia. Apparently, Melia's ancestors have long searched for a cure to a curse, and only a specific gene sequence will relinquish them from it. After the AI grants Melia a royal seal, Tyrea appears and attacks Melia.
The party survive their fall, and belittle Reyn for pressing the button. Alvis notes that they were lucky, and can still reach Melia albeit less directly. Traversing the tomb, they encounter and defeat several Orluga Rufus before reaching Melia just as Tyrea attacks her, revealing that Melia is half Homs (a surprise to Shulk). As they arrive, a large Telethia appears above them, forcing the group to fight both. After the battle, Tyrea's mask is knocked off and the Telethia absorbs too much ether. The group ends up in the blast radius, but Alvis uses another power to absorb the explosion; during the confusion Tyrea escapes. Shulk thanks Alvis and Melia, removing her mask, thanks the group for saving her, holding a happy Riki in her arms.
Melia goes to her father and brother with Alvis, and they explain the events in the tomb. Melia's coronation is scheduled to a year following Sorean's death. The party relax in their room, but Dunban is curious to why Melia is to be the next ruler instead of Kallian. 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 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 accepts. 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, a little uncertainly. Meanwhile, Lorithia and Alvis discuss a plan.
One month earlier, Alvis showed Sorean a vision of the future. The vision, similar to Shulk's, has the group fighting the Faced Mechon on Prison Island, only for Sorean to die. Sorean acknowledges this, and Alvis states it will occur soon.
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 visit her home. This is the first time she is seen with her head uncovered; her High Entia wings are smaller thn all other High Entia seen and the villa is the only place she is allowed to have them visible. After the group admires the villa's garden, Melia explains the marital practice of the imperial family; Emperors are required to have polygamy one High Entia - in this case Yumea, Kallian's mother - and one Homs - Melia's mother, who died years before the events of the game due to High Entia longevity (Melia is 88). The practice of marrying a Homs has generated controversy among some High Entia, so Melia, being half Homs, must cover herself fully when in public. Melia then invites the group to a banquet, which they gladly accept. As she begins to leave in preparation, Shulk has a vision similar to the one that Alvis showed Sorean in the latest flashback - and with the same outcome. This horrifies Shulk, who relays it to Melia just as the Mechon warning sirens begin to sound. The party rush to the audience chamber to stop Sorean, but find that he has already left.
On Prison Island, Sorean 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 - a member of an ancient, long-thought extinct species known as Giants, who greets Sorean as if he already knows him.
The party unlock the two seals required to enter Prison Island and defeat an ancient creature, transporting up to a large gate on the island. They see a statue depicting an ancient High Entia, but Reyn and Riki note that the statue resembles a Telethia. After Melia opens the door via another genetic analysis, the group proceeds. Shulk sees another vision, in which he is with the Giant, and the Giant decides to "let the shackles be released". Shulk tries to tell the group, but they cut him off.
The group ascends to the pinnacle of Prison Island, where Sorean is with the Giant. The Giant reveals himself to be Zanza, the creator of the Monado. He asks Shulk if he wants him to unlock the Monado so that he can damage Face Mechon. Shulk agrees, despite Melia's hesitations, and frees the Giant. Metal Face arrives and launches a spear at Zanza, breaking through the ether barrier and killing him. 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 his attack is not strong enough; Metal Face rises back up and Sorean pushes Melia out of the way right before being stabbed by Metal Face. As Zanza dies, Face Nemesis asks him to stop, but he dismisses her.
Shulk is furious that he could not prevent Sorean's death, but with Zanza's words the Monado changes; it becomes significantly more powerful. Shulk lunges forth with all his strength and attacks Metal Face only to be blocked by Face Nemesis, whose torso is damaged enough to reveal that the Mechon has a pilot - a Homs. The Homs removes her helmet to reveal Fiora, apparently alive but uninterested in talking to them. Metal Face and Face Nemesis retreat to avoid further damage from the Monado, to Shulk's horror as he watches Fiora leave again.
Sorean, dying, says that this was how it was supposed to be; that Melia is now the empress of the High Entia. Alvis is later seen talking candidly to the either where Zanza was killed. 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 as he is familiar with the mountain. A short-range pod takes them to Makna Forest, where they reach the passage to Valak Mountain.
In Galahad Fortress, Face Nemesis undergoes repairs while 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 to 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 Nemesis to disable it 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 Dunban's home. Dunban charges straight for him, but Mumkhar remote controls Metal Face to aim a claw at Fiora's neck, threatening her life. He then demands they surrender the Monado - which Shulk does - and beg, but Melia blasts Mumkhar and Metal Face with an ether attack, knocking Metal Face down and the Monado out of Mumkhar's hand, which Shulk takes back. Mumkhar then releases his 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 arrive in Sword Valley, Dickson greets them with anti-Mechon weapons and news of an alliance between the Homs, High Entia, and Nopon. After hearing about Mumkhar and Fiora, he departs with Alvis back to Alcamoth. The party travel through Sword Valley, until just before Galahad Fortress, where Mumkhar again is lying in wait. Dunban almost kills him but is stopped by Shulk; who points out that Fiora could be in the same position. 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, inside his Face, plummeting towards the ocean.
The group find Egil and Face Nemesis waiting to fight them at the base of the fortress. Egil disables the Monado and overcomes the group easily. Fiora begs Meyneth, still controlling her body, to help Shulk. Meyneth breaks free from Egil's control and attacks him with a power that surprises Egil; much of Galahad Fortress is destroyed and Nemesis greatly damaged. As the fortress crumbles, Nemesis slides out, and Shulk dives after her as 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. He 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 her; she wakes, saying that it was her first kiss. Shulk asks her if she remembers him, which she does, as Meyneth has receded in her mind leaving her in charge again. She explains that she could see everything happening but had no control over her body while piloting Nemesis. 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.
In the Machina village, Miqol explains that Lady Meyneth is the creator of Mechonis, and fought to defend the Machina from the Bionis. She succeeded in stopping the Bionis, but Egil is now blinded by a desire for revenge for the Bionis' attack. 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", who retains memories of Sharla. Egil deletes these as the Mechon thrashes.
The group leave the village and head 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 cannon at the party in a killing attempt.
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 explains that Gadolt has his memories erased and that the Faced Mechon are created to counter the Monado since it initially could not harm the races of Bionis. She also reveals that Zanza is the progenitor of the Homs and is the one who devastated Mechonis. 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, now known to be the goddess of the Mechonis. Shulk and the others learn that Bionis and Mechonis were once at peace, 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 notice that he is missing Sharla on purpose, and realize that he can still be saved. 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, with Gadolt asks for Reyn to take care of Sharla as he is too weak to move.
The group reach 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, he weakens Bionis itself. Shulk fights Egil, successfully impaling him through the shoulder with the Monado. He tries to reason with Egil once more, but Egil is unmoved, and removes the Monado easily. 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 from the sword. Shulk's party find themselves falling, but are caught 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 still restraining the Monado's power. Shulk begins to wonder if he should use the Monado, given what he now knows about Zanza and the Bionis, and cannot figure out why his abilities to know what comes next have changed - he has no visions, just understands what is about to happen. He experiences an abrupt seizure and 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 defeat him before he can destroy Bionis, and Shulk decapitates Yaldabaoth, leaving Egil defenseless. Shulk raises the Monado to kill Egil, convinced that he wants this despite outcry from Fiora and Vanea and encouraged by Zanza's disembodied voice, which he doesn't recognise. He remembers all that has led up to this moment and realises that he doesn't have to kill Egil - at the last minute he deflects the Monado to avoid Egil, and sits down beside him. Egil asks why he held back, as doing so would've ended the war, to which Shulk says he has forgotten that. He has realized that he and Egil are similar, and have no reason to fight. Egil says that he still has a reason to kill Shulk, and asks if he will resist killing him even if Egil kills everything on Bionis. Shulk replies that he can stop Egil, and will again and again until they see eye-to-eye. Egil considers this, and commends Shulk for using the Monado well, but asks him if he believes himself its true master. He tells Shulk of the past, when the Bionis and Mechonis lived in harmony; Arglas, the Giant possessed by Zanza, asked what lay beyond the titans, beyond even the sea. He expressed that one day the descendants of the Giants and the Machina should leave to explore and discover new worlds, and that the inhabitants of the two titans should continue living in peace for eternity. Egil 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 up the Monado, 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 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 says 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. As Shulk reaches for Egil's hand he is shot in the back - Dickson has arrived, and taken the shot.
Shulk falls and is caught by Yaldabaoth's hand. Everyone asks 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 recognises him as a Giant and Disciple of Zanza. Dickson then tells everyone to prepare for Zanza's return; Shulk's body starts glowing and rises into the air. Egil tells Zanza that he will not allow his return, and fires a shot from Yaldabaoth, which is absorbed by Shulk and fired back at Egil, damaging Yaldabaoth. Zanza, the god of the Bionis, appears out from Shulk's body as a blond man dressed in white and gold. He takes the Monado and tells everyone not to be surprised about his return, as it was predestined, and has been since he first resided in Shulk. Meyneth, speaking from Fiora, explains that after the great battle Zanza grew weak and his soul - the Monado - was sealed in Ose Tower. Dickson reminds them that he "rescued" Shulk with the Monado, having "found" the others dead, as the Monado had drawn the life from them to sustain itself. Zanza tells them that Shulk only appeared alive due to Zanza being inside him; Shulk has been dead since childhood and was chosen at random from the researchers. Dickson confirms that Shulk's ability to use the Monado and his visions, were Zanza's, and that everything that has happened has been by design. Zanza 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 that he is too weak to fight more. He claims he does not care, for he will gladly give up his life to defeat Zanza to attain peace. Zanza converts the Monado to a new form, even as the Monado appears as the sword of light in 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 own Monado, successfully protects it and Shulk and his friends. She tells Zanza that she understands that their life forms' lives are theirs to control, and if he will not accept that, she will fight for them, and she engages him in battle in Fiora's body.
Meyneth is overpowered by Zanza, who notes that her strength has significantly dropped from their last conflict. Realizing that Shulk is important to both Meyneth and Fiora, Zanza prepares to kill him, but Meyneth shields his body and takes the blast herself. Zanza tells Meyneth to face him like a god, and releases another powerful blast; Meyneth expels herself from Fiora's body and takes the full attack. She suggests that they create a world with no need for gods before disappearing, leaving only her Monado, which Zanza takes for himself. Laughing, Zanza disappears, transporting onto Prison Island, which he sinks into the Bionis' head, releasing high concentration ether waves that affect the High Entia in Alcamoth. Back on Mechonis, Vanea rushes to Egil, who apologizes for everything he is done, and insists he fulfill Meyneth's final wish. Vanea accepts his judgement, and the party escape with Shulk's comatose body.
The party leave on Junks, but Zanza intercepts tried to destroy them with the Bionis' Monado. Egil uses one of the arms of Mechonis to block the attack, and the other 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 from the ether event, Bionis moving, and the destruction caused by the Mechonis' attacks, Junks aims to get free - but as they pass between 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 from the Sword. Kallian is informed of Dickson's betrayal, and prepares to fight him. Dickson calls for Lorithia to reveal herself, and she releases high concentration ether waves from the Havres - made by her design - turning the High Entia soldiers into Telethia. Kallian apologizes to Melia for burdening her, having known that this could one day happen, and uses the last of his will to direct his Telethia form to take out Dickson and Lorithia, allowing the group to escape back to Colony 6.
Junks lands in Colony 6, Shulk unconscious in the infirmary. Fiora places a Replica Monado made for him by the Machina beside him. 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 now that Meyneth is gone. 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 life has been pointless, having been dictated by Zanza. Alvis appears and tells him only he may decide that; Zanza's need for a physical host limit him, and he must perpetuate his existence by the destruction of the world. 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 across the scene.
At Colony 6, the party fight the Telethia, but find themselves surrounded. Shulk arrives, fully awake and competent even without the Monado, and Dickson sends his own Sureny Telethia 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 defeat it, Dickson and Alvis flee.
The group uses Junks to reach the Bionis' Interior through the wound from Egil's final attack. When they reach the heart they find Lorithia, who taunts them by revealing that Kallian is still alive, albiet an unconscious Telethia. Lorithia fuses with Kallian's Telethia and the party fights and defeats her. During Lorithia's death throes Melia has a vision, where she speaks with Kallian's spirit. She apologizes for failing to protect her people, but Kallian reassures her that the High Entia's transformation into Telethia was inevitable, that she would not suffer the curse of their 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 into light along with Lorithia and tells Melia she must now live her own life and make her own choices, for that is the hope of the High Entia. Riki hears the words, and Melia hugs him. 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 pride at 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 the vision cuts off after that. Zanza wonders why he cannot see past that point, stating that with both Monados in his possession, he should be perfectly connected with the passage of fate. He realizes that both Dickson and Lorithia have died, and wonders if the Telethia weakening if they are continuing to be felled. He recalls Meyneth's dying words: wishing for Shulk to create a world with no need for gods. Zanza scoffs at this, as no world can exist without a god. He declares that the world belongs to him before imbuing himself in a mass of energy.
Upon transporting from Prison Island, the party find themselves in what appears to be a simulation of the Solar System, in which they fight silent ghosts of important encounters; Mumkhar, Xord, Alvis' Telethia, and Gadolt. 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 had planned to use his body as a dwelling place for the next millenium, but thanks to obtaining Meyneth's Monado, he can proceed immediately. He thanks Shulk for this, and offers to make Sulk a new Disciple of his. Melia calls out his arrogance and treatment of his creations, but Zanza shows no understanding, as High Entia are just Telethia given sentience Telethia are his own cells; he feels they should be grateful for what existence they had. Shulk rejects the offer of immortality, as he simply wants to live in a world without Zanza. Zanza expresses disappointment that Shulk thinks this way, but believes that the vision of mortals will remain limited. He expresses disappointment that Homs have become disobedient and in need of destruction as he deemed the Machina, saying that he had longed for friendship, but now believes that granting intelligence to his creations was a mistake. Shulk refutes this; Meyneth was able to exist with them, that she saw them as her friends; Zanza could not as he never saw his creations as anything more than food. Zanza brushes it off, saying the Telethia will eliminate every being from Bionis, and that he will create a new world as he has many times before. Shulk insists that the party will stop him.
In the ensuing battle, Zanza transforms into a third form; a god-like monstrosity, taking on the form of a Bionis/Mechonis hybrid with Telethia wings. He tells the group to behold the true form of a united world before the fight continues. Throughout the fight, Shulk still has visions, confusing Zanza as Shulk is without a Monado. Fiora 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 that such a right is reserved only for gods, which Shulk refutes; 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 Monado III. Fiora tells Zanza that he is not the only one that has the right to decide people's fates; every living being does. Zanza is shocked by the appearance of another Monado, having believed he and Meyneth held the only two in existence.
The party overcome Zanza; Alvis' disembodied voice tells Zanza that the world's providence has limited Zanza, and Zanza berates him for disobeying him. Alvis says that he - Alvis - is the Monado; he existed at the beginning, and will proclaim the end, to Zanza's disbelief. Alvis asks again if the world belongs to Zanza or Shulk, to which Shulk says that that decision was made long ago. With a mighty cry, Shulk raises the Monado III into the air as it is enveloped by light once more. Once it fades, the Monado III displays a 神 (God) symbol. Shulk declares that today, they use their power to fell a god; he charges at Zanza and swings the Monado III full force at him. The God-Slaying Sword cuts through Zanza's body, splitting him in two in an explosion of light.
After the battle, Alvis appears before Shulk as a green star, and shows him a vision of the past. Zanza was once a human scientist named Klaus; he and Meyneth performed an experiment attempting to create a new universe, but destroyed their own in the process. They were given power over the new world, and arose as the 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 own could have coexisted, which Alvis confirms was once a possibility. Alvis reveals that he was originally the administrative computer of the space station where the experiment was performed; an AI. He informs Shulk that their world is expiring, and that Shulk, as its new god, must decide whether to let the old world stagnate or evolve it to the next stage. Shulk says that he only wanted to stop Zanza, and that he himself cannot be a god.
Reyn appears from behind and agrees; the rest of the party follow. Fiora expresses that none of them want to be gods either, and that they can live life as it comes. Reyn notes the everyday life is fine for him. Sharla says that being with loved ones is enough. Melia adds that everyone changes, so no one day will be the same as the last; the future will still be unknown. Riki says it is better not to know. Fiora says that the small surprises in life are what make it great; they may be worrying, but also exciting. Dunban notes that the fact that they're still evolving is progress itself, and that they do not need a more dramatic change. Shulk agrees and says that little changes, as every day passes, should be how everyone lives, and that this is their world. He finds himself back in the Space Memory, and Alvis apologizes for interfering, saying that he recreated the others' personalities from Shulk's consciousness, because the world will collapse very soon. He asks Shulk for his final decision: Shulk simply says that he will not be the one to decide; that the future shall be decided by every being in the world - to recreate the universe without gods, and he proceeds to toss his Monado upward to Alvis. The Bionis falls and a new universe is formed.
Six months later, Colony 9 is shown; Homs, Machina, Nopon, and even High Entia now all live in harmony. The camera is in first person perspective, where a person walks down the street and is greeted by various people from Bionis and Mechonis. Vangarre is seen chastising his soldiers again. Otharon and Dunban are going over trade operations with Vanea, who muses that this is what Egil and Meyneth would've wanted. The person behind the camera, revealed to be Fiora, asks Dunban if he has seen Shulk; he says that he went with the group somewhere. As she departs, Dunban starts to say something else, but can only say "Good luck", smiling. Fiora 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.
Fiora then goes down to the new 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 protests, demanding Reyn to catch a fish for him. 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 to fall into the sea again. Fiora sees Shulk standing alone, and approaches him to sit on the beach beside him. At this point, her body is shown; she has been restored into her Homs body, retaining her short 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 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 face the future together. The camera pans out, revealing the remains of the Bionis in the sea.
One year later, Shulk tells Melia that the remains of Alcamoth have been sighted near the floating remains of the Bionis' Shoulder. The two set out to investigate in Junks alone, but are shot down by a laser attack from Alcamoth and crash land on the Shoulder. They rescue two young Nopon, Nene and Kino, who stowed away on Junks looking for heroism. They are Riki's children - Nene biological and Kino adopted - and these four comprise the party. They head to Companions' Cape, a High Entia encampment, where they meet Maxis, who is in charge. He tells them that the High Entia soldiers have been driven from Alcamoth by the Fog King, a new and unfamiliar beast that they are powerless against. Although they cannot harm the Fog King, they have repeatedly tried, as they feel they must reclaim their home. Another settlement, Gran Dell, contains civillian survivors; the soldiers have moved away as several Machina are among them, and the soldiers - particularly Gael'gar - blame the Machina as a whole for Egil's attack on Bionis. Melia suggests that she and Shulk may have the power to defeat the Fog King, so the party head there to try.
They find Alcamoth surrounded by Telethia, overgrown and full of wreckage. In front of the Imperial Palace they rescue Teelan from what they assume to be the Fog King, really only a Fogbeast Taos; upon its defeat Teelan tells them that it was not the king. The laser zaps at them again and they make their escape, accompanying Teelan to his lab on the Shoulder, where he lives with his "Big Sis". Shulk recalls that Teelan aims to discover how to revert Telethia to their High Entia selves, which Gael'gar overhears. Upon reaching the lab, they discover that Tyrea is Teelan's protector, to Melia's surprise. Tyrea speaks to Melia alone, telling her that after the destruction of the Bionis she wandered its ruins waiting to die until finding Teelan and saving his life some time ago. Since then she has dedicated herself to Teelan's research. Gael'gar is seen again to be eavesdropping, but goes unnoticed.
The party head to Gran Dell to meet Radzam, a Machina researcher known by Teelan, who tells them that the remaining Telethia are creating an ether field around Alcamoth, unintentionally sealing the Fog King inside. Radzam requests that the party bring Teelan's notes to him, and they agree, although head up the Eternal Zenith first, from where they see another rift opening up. Upon approaching it on the Soltnar Seal Island, several Ponio are affected by the Fog and become violent Fogbeasts. After defeating them the party return to Gran Dell to warn the residents, but find their Armu have become Fogbeasts already. Radzam notes that the rift is growing, and will continue affecting more creatures, potentially all of them. To prevent this the party conclude they will need Teelan's research, and head to the lab.
Tyrea and Teelan leave the lab under attack as the party arrive; Gael'gar has acquired two Andos units and attempted to murder the pair due to his belief that the pure-blooded High Entia should not be returned from their Telethia forms. Melia berates his small-mindedness and they fight, Gael'gar enraged that Melia does not side with his ideals. His is driven off upon arrival of a Telethia, and Melia rushes into the burning lab to save any research she can. Shulk rushes in after her, and they emerge with just one book - the Telethia Research. Melia, unconscious, is taken to Gran Dell and healed using water ether as she was in her first encounter with the party in Makna Forest. Tyrea scolds Melia for risking her life, although relents upon being reminded that Melia saved one tome of great importance. Shulk concludes that if he can get some high quality ether crystals, he can upgrade his Monado Replica EX to harm the Fog King, so the party set out to find these in Zekr Marga Quarry before returning to Gran Dell.
After they return, Gran Dell is attacked by a Mammut Fogbeast, which the party defeat. Melia suggests she bring the Companions back from their cape to defend Gran Dell while the party tackle the Fog King, with Tyrea defending the gate in her absence. The party arrive as a strong Fogbeast threatens the soldiers at the cape, and Melia convinces Maxis to return to Gran Dell just in time to save Tyrea's life. Radzam and Maxis reconcile, and the party set out to Melia's old home, the Imperial Villa, where Tyrea has seen the Fog King. She gives Melia her old ceremonial mask, which acts as the transporter key.
Upon reaching the villa, the party attack the Fog King (a senseless, furious monster made of fog and flames, shaped like a Guldo) but even with Shulk's upgraded weapon struggle to defeat it. Shulk notes that closing the rift may dispel its power; subsequently Telethia begin throwing themselves into the rift, their destruction destabilising it. Melia gathers her power and releases a huge wave of ether that erases the Fog King and the rift. Nene and Kino dance in joy, while Shulk and Melia deem the future safe from that threat. They return to Gran Dell, and stills over the credits show that subsequently Shulk, Nene and Kino return to Colony 9, to the delight of Riki and the other party members. They tell the residents of Colony 9 about the Shoulder while Teelan and Tyrea continue researching; after some time the rebuilding of Alcamoth begins, aided by Colony 9. Once Alcamoth is rebuilt, residents of both Alcamoth and Colony 9 gather for Melia to finally have a coronation, and officially become Empress of the High Entia.