Souichi enters Ayato’s holding room and sees he hasn’t eaten. He takes Ayato to Makoto, who he addresses as commander. Makoto explains that Jin is confined to his residence and asks if he’s afraid. Ayato says he is because he knows he can kill him for no good reason. Makoto says he’s never liked him, but he’ll still use Ayato as the key to the RahXephon. Makoto says that he’s being allowed to live at his whim. Reika suddenly appears in TERRA uniform and Makoto introduces her as a new cadet. Reika introduces herself as Haruka and says she’d like to see Ayato’s paintings sometime. Two TERRA officers moan over the missing Quon and Kim says the Foundation has her. They mention that Makoto’s also from there and that Haruka and Souichi quickly became his flunkies. Donny stares at Elvy and fails to realize he’s over pouring his coffee until it burns him. Elvy hands him a handkerchief and he jokes about how pretty it is. Ayato walks home and Mamoru comes out of the bushes. When Ayato enters the house, Megumi energetically welcomes him home. She notices Mamoru and Ayato asks about Shougo. Shougo visits Jin and thanks him for getting Ayato pardoned. Jin says he envies Shougo because Ayato’s blood doesn’t bother him. He asks how he could be more like him and he tells Jin to have dinner with Ayato. Ayato hangs up Hiroko’s wind chime and Mamoru explains that TERRA got him out, but he escaped before they put him in an institution. Megumi brings them some snacks and she says it doesn’t bother her that Ayato’s a Mulian. He says it doesn’t bother him either because he doesn’t have a choice. Mamoru introduces himself and Ayato asks she keep his presence a secret. She agrees and goes to cook dinner. Mamoru says she’s like Hiroko and looks at Ayato’s sketchbook. Shirow asks Itsuki whom a painting is of, and he replies it’s the one who holds his heart. Makoto tells Haruka she’s going to have to be very loyal to him if she doesn’t want to be punished for helping Ayato escape and he slips her a note telling her to keep him company for the night. She does nothing and he dismisses her. Helena comments on how Makoto needs to get everything Itsuki wants and that there are two kinds of men: those that make women happy and those that don’t. Makoto says the plan is proceeding smoothly.
Elvy has a beer and tells Haruka since she’s grounded, she can cut loose. She comments on how Haruka has become the White Snake’s, Makoto’s, favorite and that it’s proof she’ll do anything for the one she loves. TERRA detects the dolem Obbligato and Makoto orders Alpha Squadron to launch. Cathy, Jean and Donny go to launch and Donny tells Elvy he’ll return her handkerchief after the battle. He wonders if they could do something while she isn’t his CO. They launch in their Vermillions and engage Obbligato. It sends its sub flight dolem at them and cuts Jean’s Vermillion at the waist. Megumi relaxes in the bath and wonders if Mamoru knows a lot about Ayato. Mamoru looks out the window and says Hiroko would like the view. Ayato wonders why the sky and water are blue and Mamoru notices the drone fighters launching. The smaller dolem takes them out and Mamoru starts shaking. He begs Ayato to help him and he remembers Hiroko. Ayato says he’ll protect him and heads out. Megumi asks where he’s going and he says he won’t loose anyone else. Mamoru laughs and says he will. Obbligato dodges Cathy’s fire and impales her Vermillion with spikes from its fingers. Cathy ejects and Obbligato uses the Vermillion to shield against Donny’s attacks. Ayato cries out for the RahXephon and it launches. Elvy begs to be let into her Vermillion so she can help. Obbligato easily cuts off Donny’s Vermillion’s limbs and Ayato boards the RahXephon. He uses his energy blade to slice through the small dolem and Obbligato appears holding Donny’s Vermillion. Mamoru has Obbligato slice through it, killing Donny. Ayato charges but Obbligato avoids, grabbing his arm and waist. Ayato tires to punch it, but a third arm grows from its chest and grabs the RahXephon’s other arm. Reika asks Ayato who he wants to protect and glances at Haruka. The RahXephon uses its wing to cut off Obbligato’s arm and rip out its third one. The RahXephon aims its bow and fires, but the small dolem takes the hit. When the explosion clears, Obbligato is gone. Souichi asks for the status of all the pilots and tells Makoto that Ayato is quite useful. Ayato says what happened to Hiroko must never happen again. Mamoru clutches his arm and says that the sky and water are blue because they’re meant for those with blue blood. Haruka talks to Reika about how human relations are about common interests. Haruka says Ayato’s happiness is in her interests but that he might never realize it and she might end up alone.
Ayato returns to TERRA and thanks to Jin and Haruka, he’s pardoned for his actions. Makoto’s now the commander of TERRA and Reika randomly appears. She does what she did back in episode two and Makoto suddenly recognizes her. It’s odd she’d choose the alias of Haruka though. Mamoru also appears along with his dolem Obbligato. It’s quite powerful and easily disables Jean and Cathy. He also kills Donny, who is the second named character to get killed. Ayato promises to protect Mamoru, but like Hiroko, he goes out and unknowingly fights against him. Mamoru mentions Hiroko quite a few times and it’s obvious he knows what happened and is holding a grudge. Now that the series is approaching its finale, the death count is sure to rise.