Ayato stares at himself in the mirror while Haruka silently watches him. Helena confronts Itsuki and says that Quon has been awake for a while. She pulls out the data file Sayoko gave to Makoto, and Sayoko says he said he would use it to help Itsuki. Sayoko says it was for his sake, but Itsuki says it was for her’s. Sayoko runs out and Helena asks where Makoto is. Itsuki says he doesn’t like dealing with her, and a sample of blue blood is taken from Quon. Haruka meets Johji at the shrine and tells him the Bahbem Foundation is taking over Quon’s care. Johji repays her for the tip by telling her Shougo had a daughter. He says she moved out and got married, changing her last name to Kamina. Johji suggests she ask her uncle about it. Elvy test flies the Vermillion and says it handles like a baby. Jin asks if it’s all right, and Shirow says that it was provided by the Foundation so they couldn’t refuse. Elvy uses the wave optical cannon Baus-Ghazal to destroy a small island and Helena asks why she hasn’t seen Ayato around. Elvy lands and Cathy tells her how amazing she is. Souichi asks them where Ayato is, but they haven’t seen him. Elvy says that they could easily take out Tokyo Jupiter with a hundred Vermillions, but Souichi wonders why TERRA needs it. Elvy asks to speak with him, and they both go into a hanger. Elvy asks him what he meant, and Souichi says that since TERRA’s purpose is defense, they don’t need the Vermillion. Elvy asks about Operation Overlord and he says it was carried out by the Federation and that he was against it. She asks if he fought it or just bit his tongue and calls him a hypocrite. Cathy asks Ayato what he thinks of the Vermillion, and he says it’s great. She tells him Souichi was looking for him and that he went to talk to Elvy. Souichi asks Elvy how many innocent people she killed in Tokyo and she says they were just Mulians. Souichi says they’re no different and asks if Ayato is less human than she is. Elvy is shocked and demands he repeat himself. Souichi says she should forget what he said and they turn to see Ayato. He apologizes and runs off, but Souichi chases after him. He finds him and Ayato asks what he is. He asks if he was the only one who didn’t know, and Souichi says only a few people knew. Ayato asks if they were laughing behind his back or just using him. Souichi calls himself pitiful because he can’t smack some sense into Ayato’s head. Souichi says where he comes from doesn’t matter but Ayato snaps that words can’t change anything. Souichi says they can when people talk to each other, but he gets a D1 alert. Ayato says he’ll fight but Souichi says he doesn’t have to and asks if he can fight in his current state of mind.
Elvy launches in the Vermillion and thinks of how she wanted to give Ayato a choice, but he’s a Mulian. Jin asks where Ayato is, but Souichi shakes his head. Elvy engages the dolem Alternate and shoots it into the water. Ayato thinks about what people have told him in the past and reminds himself that he fights because he can. Alternate splits into two and surrounds Elvy. Ayato says he’s ready to launch and Helena thinks a joint Vermillion RahXephon battle would provide good data. Makoto asks Itsuki about Helena, and he says she was eager to see him. Makoto says the three of them will have to meet. Alternate flies around Elvy and the RahXephon arrives. Elvy tells Ayato to get out of her way, but Ayato says he’ll fight. Makoto asks Itsuki to understand why he gave Quon’s data to Helena, but he says he doesn’t want to. Makoto says he’ll get used to being alone and says it’s independence. Alternate traps Ayato and Elvy in an illusion that sends back their attacks. Ayato tells Elvy to stop, but she says she can take care of the dolem on her own. Ayato asks if it’s because she doesn’t want help from a Mulian, and she says she doesn’t know if she can trust him. Itsuki says Makoto wants to open a new world using Quon as the key, but he doesn’t belong there because of what he is. Makoto throws his drink at Itsuki, telling him not to say it. Ayato sees Reika, who tells him he won’t reach Yolteotl if he looks into it. Reika has the RahXephon draw its bow and Ayato asks how she can be there when she died. She says it only appeared that way and he asks who she is. She says she is Ixtli, Reika and Ayato. The RahXephon aims at Elvy and Ayato tells it not to shoot. It fires and the arrow bounces of the Vermillion and destroys Alternate. Elvy gets mad he shot her, but Ayato says it wasn’t him. They take aim at each other but a bring light envelopes everything. Itsuki asks Makoto if he felt something but he says it must be the alcohol. He says that Itsuki will get used to being lonely and that it’s called independence. Alternate attacks, but Elvy uses the Baus-Ghazal and destroys them. Elvy says they can win without the RahXephon and they don’t need Ayato to fight their battles for them anymore. Haruka asks Helena if she got enough data, and she says 38 minutes is plenty, but Haruka says it was only 20 minutes. Later, Ayato smashes his mirror in anger.
Elvy gets her mid series upgrade this time and she handles her new Vermillion with great ease, taking out a dolem by herself. Elvy finds out Ayato is a Mulian, and she doesn’t take it very well. Ayato finds out too and now he feels like the odd man out. Haruka finds out something interesting about her uncle and he is somehow related to Ayato. The RahXephon again shows how god like it is by actually turning back time. While no one else is the wiser, Helena seems to be aware of it. Now that Ayato thinks he’s not needed anymore, there’s no telling what he’ll do next.