After Celebrating New Years, it's back to the beach. Quon wanders off, and Ayato follows her. They come up to ruins located in the forest. Apparently Quon and Ayato go missing, and and Haruka starts a search to find them. Quon and Ayato are off somewhere, and Haruka's search was stopped due to the fact they were no where to be found. Haruka ends up back at the ruins, where Quon and Ayato reappear in front of her again.

B-story line: While Ayato and Quon are missing, Itsuki tries to pilot the RahXephon, but fails to do so.

A dolem is beating RahXephon, and Ayato is writhing on the floor of the cockpit, and is in a dream state where, Toyko is much different, there are flashes of a Murian, Mamoru, Hiroko, Haruka Mishima and his mother.

Itsuki, Helena and Isshiki grew up together as students of the Bohbem Foundation. While many of the other students exhibited special abilities, Isshiki showed little talent and was considered to be normal. When Isshiki finds a stone-like creature, his desire to protect it awakens something within him that he never realized he had.

The aerial cities continue to multiply. Kunugi decides to evacuate everyone from the island and stay by himself to try to stop the D1 headed their way. TERRA leaves with everyone else. The D1 is the Dolem of Kuki, Kunugi's former superior officer that gave him the order to kill his own daughter. It reaches the island of Narai Kanai and starts destroying cities. Kunugi sends some missiles and remote control fighter jets, but they do no good. The D1 attacks the building he's in while Kuki taunts him. Kunugi is injured, and Kuki says it's over. But Kunugi tells him that the entertainment has yet to begin, and activates the barrier creating thing. The barrier destroys everything in it's path, including the cities, Kunugi, Kuki, and the D1. Ayato makes a choice to join with Ixtli in order to protect Haruka.