For those who have not completed games in the Xenoblade Chronicles series, this page contains spoilers regarding the plot. Discretion is advised.
Mikhail spends much of his time working on the systems of the Marsanes, the sole remaining Tornan warship which acts as the organization's base, preparing it for the inevitable confrontation with Amalthus. At the World Tree, before Jin and Malos are dropped in the boundary layer, the Indol Titan emerges from the Cloud Sea and attacks the Marsanes. Alongside these battle Indoline Stars and Blade Bots. After a fierce battle, Mikhail orders Patroka and Akhos to follow after Jin and Malos, and transforms the ship into a Titan-sized mech resembling a Faced Mechon which he uses to fight against Indol directly.
During the fight Rex, Pneuma and Poppi α attack Indol using Siren Buster at Indol's amp towers, destroying them and preventing Amalthus from controlling Blades and the other Titans. In retribution, Amalthus tries to kill the party with one of Indol's Ether Cannons, but the Marsanes blocks the blow with its back. After Mikhail has a final talk with Rex and Nia, the Marsanes flies towards Indol, grabs it by its neck and throws it against the World Tree. In its final moments, Indol tries to fire a massive Ether beam from its mouth, but the Marsanes charges fist-first towards it. Their clash destroys both the ship and Indol in a massive explosion.