With Japan in ruins, the survivors begin to pick up the pieces of their shattered lives and try and slowly rebuild. At the same time, Ayato appears amidst some rather heated emotions, and Quon makes her final move.
Tempers and attitude flare as Isshiki`s take-over of TERRA begins to take its toll; Mamoru finally learns what happened to Hiroko when she came over with Ayato; and Isshiki reveals his plan to take down the barrier around Tokyo for good.
Ayato is back with TERRA again, but now Isshiki is in charge, and that`s not good; Mishima has suddenly appeared as well; and Mamoru seems as though he`s ready to accept what lies beyond the only world that he knew.
Ayato continues to confront each and every person that he encounters about how long they knew the truth about how and what he is. Unhappy about the situation, and that he has been lied to, he toys with the idea of returning once again to Tokyo Jupiter.
The present becomes the past as the focus shifts to the Bahbem Foundation. Three young children live there as students, but Isshiki has found a Dolem living in the ruins beneath the mansion and wants to protect it.
A shake-up at the base takes place when the corporate interests use their influence to take charge of Quon; and a new Terra weapon, the Vermillion, debuts and it's made clear that the Foundation have agreed to let TERRA use it.
The question on everyone's mind is just who Quon really is: Itsuki claims that she is his sister, but things come to light that make him seem like a liar. Meanwhile, the latest toy from Bahbem is tested both on and off the battlefield.
A crystal given to Sayoko by Kisaragi has some adverse effects when Sayoko finds herself as part of another Dolem; and the temperature on Nari Kanai changes from tropical to winter. Later, Ayato must choose between destroying the enemy and saving Sayoko.
The media pick up on the fact that TERRA has a new weapon in their fight against the Mu; Kim has memories of tragic events that led to her joining TERRA; and a reluctant Ayato once again pilots the RahXephon against an invading Dolem.
Having taken care of the Dolem threat, Ayato has proven that he can be trusted and is taken to a new home. At the same time, the RahXephon is showing signs of petrifaction, possibly due to Ayato's feelings towards the TERRA members.