Bahbem comments that Quon’s sound is getting clearer and Helena asks about Makoto. Bahbem says he’s merely a child playing with matches. He tells Helena it’s her time and her younger self reaches out to her. Makoto fires Haruka because of her doodle and Souichi calls her a lucky dog. Makoto gets a message from Federation headquarters and decides to move the operation ahead an hour. He adds that he’ll command the operation from onboard the Lilia Litvyak. Ayato works on a painting and Megumi says they should stop letting what happened with Mamoru bother them. Ayato agrees and Megumi wonders where her sister is. Ayato guesses TERRA and Megumi tells him she got fired. She looks at his painting and asks who she is. Ayato wishes he knew himself. Megumi picks up Haruka’s belongings from TERRA and takes a peek at an old picture. Megumi is shocked to see it’s of Haruka and Ayato and says it isn’t fair. Ayato gets a phone call and goes to Jin’s place to pick up Buchi. He notices Jin’s bird and asks its name. Jin says it’s Michiru and it was his daughter’s name. He adds that without Haruka, Ayato could have been executed. Ayato asks if Jin’s cherry trees really blossom blue and he laughs it off. Jin invites him to dinner and Ayato accepts. Shirow and Shougo meet at the shrine and Shirow laments over giving Quon and the black egg to Bahbem. Shougo says everyone has to walk a different path and talks about how Maya realized she was also a sleeping beauty when she was 17, but awoke too soon. Shirow says he thought it was the right choice and Shougo tells him not to blame himself. Sayoko gives Haruka information about her dealings with Makoto and says she has bad luck with men, even her brother and father. She says she killed them and the Foundation people had said they would be fine. She adds that her life is like a piece of toast always falling buttered side down. Haruka assures her Itsuki still thinks of her as a friend and Sayoko snaps because she has to call him doctor. She says she hates Haruka, but used to hate her more. Haruka says she knew it and that she was a fool. Shirow says that an instrumentalist will loose his qualification when he’s 17 and Shougo says he just wanted to connect to Ayato as family since he’s his grandson.
Ayato works on his painting and tells Haruka she can stop hiding. Ayato apologizes for avoiding her and asks if she’ll be the first one to see his painting when it’s finished. She says sure.The arrays set up and Makoto calls for Operation Downfall to begin. The Probability Resonance field activates and Ayato paints haggardly while Quon does the same on a piano. Tokyo Jupiter dissipates and they receive a massive amount of communication signals. Ayato finishes his painting and Reika appears, saying he finished his world. Ayato appears to Quon and identifies himself as Ixtli. He says he takes the form of her heart’s desire and Reika explains she is the song of Xephon. Ixtli Ayato says it’s time they became one and Quon accepts. Reika says she is his guide and says his painting is the world they will create together. She says together they will obtain Yolteotl and become the heart of the world. Ayato refuses and says he didn’t paint it for her. Reika says he must and she goes into the painting to await him. Reika sings and the RahXephon activates, busting out of TERRA. Makoto revels in his victory but Mulian cities appear in vast numbers all around the world. The RahXephon forms giant wings of light and Quon’s egg cracks. Ayato slashes his painting, causing the RahXephon to petrify and turn back into an egg. Makoto wonders what happened and Souichi gets a message from the Federation to relieve Makoto from duty. He says he ignored the Federation’s cancellation order and Makoto accuses Souichi of setting him up. Souichi says he set himself up nicely and Makoto calls for Haruka. Souichi says he fired Haruka, but Makoto means Reika. Souichi says there’s only ever been one Haruka and Makoto cries that he doesn’t want to be alone. Haruka rushes home and Ayato says it’s not the painting he wants to show her. Quon says that Ayato rejected Ixtli and Bahbem says it’s fine because she has obtained Yolteotl. Helena steps out of the shadows and tells Quon to sing for her.
Pandora’s Box is opened with horrible results. With Tokyo Jupiter gone, the Mulians have covered the world with their flying cities. That’s certainly a RahXephon sized egg in Makoto’s face. Reika explains who she is and she’s actually the soul of the RahXephon taking on the form of Ayato’s true desire. Ayato rejects her and the RahXephon has gone back into hibernation. Quon on the other hand accepted Ixtli and obtained Yolteotl, which is the Aztec equivalent of enlightenment. With the final battle on the horizon, one question remains: does hope remain in the box?