A news report talks about the flying cities covering the world and that people are beginning to riot. Jin grabs his bird and goes back to TERRA. Everyone welcomes him back and he tells Haruka that he invited Ayato to dinner. The alarm goes off. Ayato burns his picture and Shougo sees a ghostly figure. Reports of similar sightings pour in and Itsuki says their worlds are beginning to meld. Kuki’s figure appears in the command center. Later Haruka briefs everyone on Kuki’s identity and shows them a video from earlier. On it, Kuki talks about being free from time and thanks them for their help. He orders them to disarm and surrender or else. They show a video of a city being destroyed by the massive dolem Largo. Itsuki also talks about how the RahXephon has seemingly encased itself in a dimensional barrier. Cathy wonders what they should do and Souichi says they’ll fight to the end. Jin makes a decision that Souichi isn’t happy about. He protests but Itsuki says Jin won’t change his mind once it’s set. Jin asks about Kim and Souichi says he’ll protect her. Jin says to protect her as he says and Souichi starts crying, saying it isn’t fair. The citizens of Nirai Kanai are evacuated and Jin visits his daughter’s grave. Shirow asks if he’s sure and Jin says he’s grateful Shirow asked him to join TERRA. Itsuki leaves his house and leaves a painting of Reika behind. Ships attack Largo, but are easily destroyed by its beams. Mamoru comments on how aggressive Kuki is and asks Maya why he wasn’t chosen. She says it isn’t his role and Miwa asks if what they’re doing is right. Allegretto’s pilot puts a hand on her shoulder and Maya says they are doing what’s right. The TERRA crew leave the island on a ship and talk about how they’re going to have to get off. Megumi tells Kim she’s going to need to tell him before then. Buchi sees Reika in the crowd. Elvy joins Ayato and they agree that Nirai Kanai wasn’t a bad place. Elvy tells Ayato to take a look at his guardian angel because she’s always been looking after him. Largo approaches Nirai Kanai and the automated defenses attack but are easily destroyed. The drone planes are launch and Elvy wonders if they’re being controlled from the ship. Souichi says they aren’t and Elvy notices Jin’s bird. Jin controls the drones from TERRA headquarters and Kuki’s image appears, saying he’s hard working as ever.
Largo shoots down the drones and Kuki says it’s a pleasure to see a subordinate go up in ranks. Ayato sees Buchi and runs after him, eventually finding Reika. Itsuki sees them and Reika says she wants something. Ayato follows her and winds up at the shrine and Itsuki sees they’ve vanished. Kuki goads Jin by talking about how he killed his own daughter and Jin fires all the missiles. They’re all shot down at once and Kuki says it’s useless. Ayato asks where they are and Reika says it’s the passageway where the instrumentalist will join with Xephon. She says the chosen Ollin will pass through and tune the world. Ayato says he never wished for her. Kuki laughs madly as Largo destroys Nirai Kanai. Reika says if the world isn’t tuned it will be turned to mud and that if he doesn’t want her, all will be lost. Largo hits TERRA HQ and Jin is knocked away by the explosion. Jin watches the picture of his daughter burn up and stumbles back to his consol. Kuki says he didn’t do too bad and the dull game is over. Jin says it’s just beginning and he activates the Jupiter System. Kuki says it isn’t possible and fires at Jin. Jin pushes the switch and an absolute barrier envelops Nirai Kanai, destroying Largo and killing Jin and Kuki. The crew of the Lilia Litvyak salute and Shougo and Shirow mourn. Mariko starts crying and says she just feels like something happened. Haruka watches the Jupiter phenomenon and Itsuki says the one she cares for is most likely inside it. Reika begs Ayato to want her and he says it’s the first time he’s seen her afraid. He says it makes her more human and that he was afraid too, but she was always with him. He says there’s something he wants to protect and pulls her into a hug. He says he wants her to protect Haruka with him. Reika says he’s very warm. Itsuki says there’s no doubt Ayato will be back and the RahXephon starts singing. Helena asks who Quon was playing for and she says a lost friend. She says goodbye and starts singing. Maya says Quon is coming back and calls her big sister.
This was quite the episode. Everyone abandons Nirai Kanai save for Jin who stays back to fight off Kuki, the man that gave the order that caused his daughter’s death. Earlier in the series, Jin told his daughter she wouldn’t be alone for much longer and that foreshadowed his inevitable demise here. He has a heroic death, killing Kuki with an absolute barrier. On the other side we have Reika begging Ayato to accept her. After seeing a human side to her, he agrees and the RahXephon is revived once again. With just three episodes left, anything could happen.