Haruka sings and says her and Ayato used to love that song. She starts crying and Megumi says she’s stronger than that. She tells her not to give up because that’s not what the Haruka she’s always wanted to be like would do. She says if she looses something she has to go find it. Haruka runs off and Megumi gives her a thumbs up. Human Ayato wakes up and wonders if he died or was born. Ayato sees a subway station and hears singing. Ayato goes down and finds Quon on the piano. Ayato feels like he knows her and asks who she is. He asks if she knows him and says no one does. He says that means he doesn’t know anyone and Quon says that’s how he avoids knowing. Xephon Quon attacks Xephon Ayato but he’s protected by a barrier. Itsuki points a gun at Helena and says they should be punished. Helena wonders if they should be and says she loves him. Sayoko runs up and stabs Itsuki. She cries and apologizes but Itsuki says he’s glad it was her. Sayoko says she loves him but he sees her as Quon. He says he found his blue bird of happiness and dies. Helena says she’s surprised because although she programmed Sayoko to love him, she didn’t expect that kind of behavior. Helena calls her version 7.34 and Sayoko says it isn’t true. Helena tells her to discard her false memories and see the truth. Sayoko continues to deny but Helena speaks in Bahbem’s voice, saying she just doesn’t want to know. Sayoko goes for the gun while Shirow releases Jin’s bird from its cage. Maya cries that she can no longer lead Ayato and sees Haruka in a jet. Human Quon tells Ayato he can come out of his cage. He says he would always run away and hated himself for it. Quon tells him to just accept the world and hugs him. Ayato says he won’t run anymore but that he doesn’t know what he should do. Quon tells him to trust in her and to be gentle. Xephon Ayato attacks but Haruka flies in the way. She is killed along with Maya when the blast hits the mulian city. Human Ayato gets on a train and sees Haruka before the doors close. He asks if some one was there and Quon says she needs to show him the truth. Ayato feels that some one said that to him before.
Helena leaves the church and Johji says she leaves a lot of dead bodies in her wake. Helena says that’s what’s called history. Johji calls her Bahbem and asks what he needed to see so badly that he’d resort to snatching bodies. Bahbem says Helena was quite happy to give him her body. Johji asks if the Vermillions were a part of his system and Bahbem says they were for insurance. He says he created the RahXephon system back when he was with the Mu and he just wants to see its conclusion. Johji wonders how long ago it was and Bahbem says it was tens of thousands of years. Johji asks what will happen next but Bahbem says he just created the system and it’s up to Ayato and Quon to decide. Johji says he’s acting like a god and Bahbem says since the world is operating on the system he created, he is god. Haruka wakes up in a room with Maya and Maya says if she didn’t exist Ayato wouldn’t have had to suffer as much. She says she should have been the only one to love and support him. She says it wasn’t meant to be because he discovered his own world that Haruka was in. Maya tells her to hurry and to suffer with Ayato for her. She asks her to take care of her son and points to the old middle school. Ayato finds himself on a strip of road surrounded by water and a phone rings. Quon says it’s for him and he hears Megumi’s voice. He turns around to see a TV with Megumi on it and she tells him she loves him. It changes to Hiroko and she also says she loves him. It changes to Elvy and she says while he might be a Mulian, he’s her comrade in arms. Souichi appears and says he used to be like Ayato, but he managed to connect with others because he found some one who saw the real him. Ayato says he doesn’t have some one like that but Souichi says he just hasn’t realized it. Quon tells him to free his mind and the TV shows events from Ayato’s life. It then shows Haruka saying she has to see him. Quon is surprised by a call from Itsuki. He says his brother was always chosen over him but he wanted Quon to love him. Xephon Quon knocks Ayato to the ground and her black wings grow larger. Human Ayato finds himself in a classroom watching his younger self listening to Haruka on the piano. Ayato says he remembers and Quon tells Itsuki she should have accepted things as well. She says she accepts both of them equally. Adult Haruka appears and Ayato says he found what he lost. Quon says she’s happy for him and young Ayato and Haruka kiss. Xephon Ayato grabs Quon and knocks her to the ground, his white wings growing huge. Ayato assimilates Quon and glows with a bright light. Bahbem looks on and says it’s what he’s been waiting for. Johji says he must be quite happy with himself and shoots him. The entire planet is encased in an egg. Haruka talks to Megumi on the phone and tells her their daughter, Quon, is full of energy. Twenty-nine year old Ayato finishes a painting of a girl on a cliff and Haruka congratulates him. Haruka asks who the girl is and Ayato says she knows. Several years ago, Ayato sketches the girl on the cliff. She turns around and he apologizes for bothering her. She asks to see and says he’s pretty good. Ayato asks if she’s from around there but she says she’s from Tokyo. Ayato says he is too and that his dad is there investigating some ruins. The girl says her uncle is too and Ayato asks if she’s Shougo’s niece. She says she is and Ayato introduces himself. The girl introduces herself as Haruka Mishima.
Thus is the end of RahXephon, and what an ending it was. First off, Haruka, Maya, Sayoko, Itsuki, Bahbem and Quon all meet their ends. However, Quon guides Ayato to remembering his true self and thus allows him to tune the world. When tuned, the world is recreated, so even though a lot of people died, they’re all brought back. Ayato creates his ideal world where the Mulians had never invaded and he was free to live his life with Haruka. It was all just beautifully done. RahXephon is a series constantly being compared to others, but as with any series, it’s not fair. If you’re too busy drawing comparisons, you’ll miss what it has to offer. RahXephon isn’t for everyone, but those who enjoy deep thought provoking series that are exciting to watch, this is a series for you. Not everything makes sense, but the movie clears a few things up. If you like this genre, RahXephon is definitely a must see.