When you're ready, talk to Miqol to depart back into the Mechonis. The party flies in on Junks using a passage on the back of the titan. The party lands at the Ventilation Conduit. Reaching the Bridge to Apocrypha, there is a splitting path: you can either move forward, or head down to find a teleporter leading to the Face Maintenance Bay in the Central Factory, allowing you to finish anything related to the area, such as Quests or the Collectopaedia that you might not have already. You can also return to Agniratha in this way.
Apocrypha Generator[edit]
Reaching the generator, the entire area starts to shake; the Mechonis' functions have been fully restored, and Egil strikes the Bionis. Before they can move on, however, the party is confronted by a guardian Mechon (also called the Apocrypha Generator). The generator opens the battle with Shield Barrier, granting it increased defense against both physical and ether attacks. Most of the generator's Arts are attacks that deal status effects. Magnetic Field: First and Magnetic Field: Zero decrease strength, physical defense, and ether defense. Talent Absorb absorbs the Talent Gauge. Laser can topple and its Talent Art, Great Laser VI, can inflict paralysis. Finally, the Apocrypha Generator does not drop treasures, but it carries Ether Cylinders that can be stolen using Riki's Yoink!
After the generator is defeated, the Apocrypha is disabled and the Monado is restored to its full power. At this point, Shulk gains a new Monado Art: Cyclone, an area of effect attack that can inflict Topple.
Egil[edit]
With the generator deactivated, you can finally reach the Mechonis Core using a teleporter. Note that once you proceed, most Timed Quests (primarily quests in Alcamoth, the Central Factory, and Agniratha) will expire. You will also be unable to return to any location on Mechonis, with the exception of the Fallen Arm.
Inside the core the party confronts Egil inside his Yaldabaoth, upgraded to control the Mechonis. Egil strikes the Bionis a second time before engaging in battle. Throughout the battle, Egil will use Manufacture Drones to summon additional Mechon, namely Offensive/MOTORs and Exterminator/CLOCKs.
When Yaldabaoth's health is below halfway, Egil uses Energy Replenish to grant himself full invincibility and summon three Energy Devices. A vision is also displayed of Yaldabaoth and the Mechonis using Bionis Slash X to cleave directly through the Bionis, and a new Story Quest titled Save Bionis appears. To complete the quest, and thus stop the vision from taking place, you must defeat the three Energy Devices within the vision's time limit (120 seconds); if the vision is not stopped, the attack will go through and the entire party will be automatically defeated. When the quest is cleared, Yaldabaoth's invincibility will be broken and he will be Dazed.
Zanza[edit]
When he is finally defeated, Shulk is ready to kill Egil, but is able to stop himself right before. Egil then explains more of the history of Bionis and Mechonis, that his friend Arglas took the Monado and was possessed by Zanza, leading him to attack Mechonis. As Shulk and Egil are about to make peace, however, Shulk is shot in the back by Dickson, causing Zanza himself to appear from his body. Dickson and Zanza explain everything: after the battle between Bionis and Mechonis, Zanza's soul was trapped in the Monado, and when the Monado expedition team found Ose Tower they were all killed by Zanza to keep his soul alive. Zanza then possessed Shulk, becoming Shulk's life force and enabling him to both use the Monado and see visions, guiding them to this very moment. Finally, they explain that in order for Zanza to continue existing, he plans to destroy and recreate the world. Zanza then revives the Bionis, and both he and Egil battle, though Egil is easily defeated.
As Zanza is about to destroy the party and Mechonis, Mayneth fights Zanza, manifesting her own Monado. For this battle, Fiora is the only party member available, using Mayneth's Monado as her weapon. Zanza is immune to most statuses, and attacks using various Monado Arts. In addition to the high-damage Monado Buster and Ether Field which ignores defense, Monado Brave increases his strength and ether, Monado Eater removes any buffs from Fiora and inflicts Bleed, and Monado Shield grants Zanza full invincibility. The battle automatically ends after some time passes.
Zanza once again sends an attack that will destroy the entire party, but Mayneth appears from Fiora's body and sacrifices herself to save them, telling them, "Create a world with no need for gods." Zanza takes Mayneth's Monado and leaves, beginning the process of destroying and recreating the world by sinking Prison Island and forcibly transforming many High Entia at Eryth Sea and Alcamoth into Telethia.
With Shulk out cold, go all the way back to Miqol and escape on Junks.