RahXephon

Ayato has returned to see Haruka...for the last time. He has become a God and now must battle Quon, who has also obtained the form of a God, in one last battle. The winner will create the world of their choosing. As Haruka and Megumi watch the battle begin from afar, Haruka feels lost. Megumi helps her sister by telling Haruka that she always wanted to be as strong as her. With her strength restored, Haruka commandeers a jet and flies high into the sky to see Ayato one final time.

In his last act, Commander Jin Kunugi destroyed the Dolem linked with Colonel Kuki by creating a barrier around Nirai-Kinai similar to the one that had enclosed Tōkyō. Inside the barrier, there is only one person now alive on the evacuated island: Ayato Kamina, who, having been summoned by Reika Mishima, is inside the white egg. This time, he accepts her and his destiny as the Rah of the Xephon. However, Quon, who has returned to the Mulians, has also accepted her destiny as Rah of the black egg Xephon.

Ayato has a face-to-face encounter with Mishima who reveals her true purpose for showing herself. Isshiki and TERRA initiate their plan to take down the Tokyo Jupiter barrier, but the results endanger the world.

Makoto fires Haruka for drawing a humourous caricature of him as a white snake, what he is called behind his back by the TERRA staff. Fortunately, Haruka couldn't be happier to be free of the new commander's grasp. The Bähbem Foundation, the real controllers of the Federation, have ordered Isshiki to cancel his operation to destroy the Tōkyō barrier, but Makoto refuses and moves up the operation before the Foundation can act.

Makoto Isshiki commences preparations for Operation Down Fall, which will destroy the Mulian's barrier over Tōkyō. To ensure the operation's success, Isshiki visits Ayato to make sure that the RahXephon pilot will stay loyal to his keepers. As TERRA moves towards the start of their operation, Mamoru Torigai explains to Jin Kisaragi the nature of the Mulians.

Ayato has destroyed a Dolem who, unbeknownst to Ayato, had actually been linked with Hiroko, which caused her death. Just when he felt like he knew what he piloted the RahXephon for, his world is once again turned upside down. The RahXephon pilot is returned to TERRA, now under the direction of the Federation and Makoto Isshiki. Haruka has also been promoted to an intelligence operative for Isshiki. Also joining TERRA is a person who looks just like Reika Mishima. Her name is Haruka.

Ayato and Hiroko leave Tōkyō followed by Elvy and Haruka in the Vermillion. While TERRA and the Vermillion search for Ayato, the instrumentalist and his friend, who is seeing the rest of the world for the first time in her life, make their way to Kagoshima. Trying to figure out what to do, Ayato and Hiroko each explore who and what they are.

Accompanied by Elvy, Haruka visits the middle school where she first fell in love with Ayato so many years ago. Meanwhile, Hiroko's encounter with Ayato for the first time in a month has left her visibly shaken. She feels that her memory has been altered, but she can't figure out what was taken from her. As Haruka and Elvy walk towards Ayato's house, and as Hiroko wonders about who she is, they all hear Ayato's screams in the distance.

Ayato has decided to return to Tōkyō. Quon, who is a Mulian like Ayato, will be returning with him. Without TERRA's knowledge, they head out in the RahXephon. Makoto Isshiki relieves Jin Kisaragi of his post as commander, and takes over the operation to retrieve the RahXephon at all costs. With orders to bring back the RahXephon and its pilot, Elvy moves in with the Vermillion...with a friend along for the ride.

Ayato, having learned for the first time since he left the protective barrier of Tōkyō Jupiter that he is a Mulian, has become distraught by the news. Now, without his knowledge, those in power have decided to move past Ayato and focus on Quon's talents. Meanwhile, Haruka confronts her uncle about what she has learned about Ayato's mother, Maya.

Fifteen years ago, three children are put through music training in a large mansion. The Master, who will choose one of the three to be his successor, will decide their role in what is to come. While the Master is away, the children sneak out late at night to see a creature made of mud that sings in the caves below the mansion.

Ayato's experience with Haruka in the dreamscape ("NightMare") along with seeing Itsuki Kisaragi passionately kiss her before his eyes ("Sleeping Beauty") have caused a rift between Ayato and Haruka. A rift has also formed between Itsuki and Sayoko when Helena Von Bähbem reveals that Sayoko gave Makoto information about Quon's recovery that Itsuki had kept hidden. Meanwhile, Jouji's snooping has piqued Haruka's interest, and she meets with him to exchange information.

Haruka begins a clandestine search for records pertaining to Quon Kisaragi, the first person to exhibit signs of the Mu phase. Meanwhile, Itsuki and Makoto begin to make preparations for the arrival of a visitor from the Federation just as a new Dolem appears in orbit. TERRA readies itself for battle, but the Dolem continues to stay just out of reach.

The Dolem that trapped Ayato in a mindscape has had an adverse effect on Quon: She suffered intense pain when Ayato was swallowed up by the Dolem and is now in a coma. Ayato's experiences within the mindscape have made him doubtful about his place outside of Tōkyō. Meanwhile, Elvy has begun to question her role in TERRA, and Sayoko and Makoto begin a relationship mutually beneficial to both parties.

When Ayato intercepts the latest Dolem, the large mecha encapsulates the RahXephon within itself, causing Ayato a large amount of pain. As TERRA looks on helplessly, the large Dolem swallows up Ayato and the RahXephon. Moments later, Ayato awakens...and he's back in Tōkyō.

Ayato's RahXephon and Elvy's fighter squadron successfully put down the most recent Dolem attack. Afterwards, a brief respite from battling the Mu allows the people of Nirai-Kinai and the rest of the world to honour those who died in the Great Mu War. As preparations take place, Quon plays a musical piece on her violin that stirs up distant memories for Commander Jin Kunugi.

Jouji Futagami begins to research the history of Nirai Island and comes across some information on a small shrine where it is said that two girls were reverse spirited away. As he examines his information, Sayoko Nanamori does some research of her own on the Observer: Makoto Isshiki. Meanwhile, a day at the beach for most of the TERRA staff finds Ayato contemplating his place outside of Tōkyō Jupiter. While on a boat with Quon, they both see Reika Mishima high above them on a cliff. Ayato and Quon examine the area where they saw Reika, and find a small shrine carved into the island.

While the reporter Jouji Futagami is allowed to snoop around the RahXephon, Itsuki Kisaragi finds a small diamond embedded in the spike that had pierced the RahXephon in the last battle ("Phantom in the Cloud"). Meanwhile, Christmas is fast approaching and the TERRA crew plans for a bit of relaxation in the warm weather. As a gift, Itsuki gives his assistant Sayoko the diamond stone as a present...and the weather begins to turn ice cold.

With all the rumours circulating about the giant beings attacking cities once again, TERRA Director Shirou Watari invites a reporter to Nirai-Kanai in order to see firsthand the operations of the anti-Mulian forces. Jouji Futagami of the Amato News, the one who raised the most questions in a recent news conference ("Long Songs Forgotten Melodies"), has been chosen to report on TERRA's operations. While Ayato tests out a new system, a relic found in an ancient shrine that is designed to help him synch more easily with the RahXephon, Mr. Futagami takes a stroll on his own around the island.

Fourteen years ago, a Mulian Dolem destroyed 8 cities on the continent of Australia. For TERRA Lieutenant Kim Hotal, the fight against the Mu is personal. Having lost her parents in the attack on Canberra, Kim has dedicated her life to destroying the Mu. When the Mu that destroyed the Australian cities reappears, Kim must trust Ayato to pilot the RahXephon so she can have her revenge for the loss of her parents. There's just one problem...

A cryptic message on the back of a picture of the "RahXephon" in battle leads Ayato to meet with the person who had helped him escape from federal agents ("OVER LORD"). The woman and he break into a military facility and commandeer a fighter jet. As they fly away from the facility, the jet's thrusters turn off and they are propelled to an opening that leads them to the giant mecha RahXephon...and a way out of the last city on earth.

Ayato and the girl named Reika Mishima, the girl who looks exactly like the one from his painting, discovered the ruins of Old Tōkyō. There, they located a large white egg in the centre of a circular waterfall. Ayato, overwhelmed by a strange power, spoke the word "RahXephon". Suddenly, the egg burst open, revealing a large mecha. However, that is all that he remembers. He wakes to find himself in a hospital. The invasion has been repelled, and Ayato sits among the wounded civilians from the attack, waiting for his mother to pick him up.

Ayato Kamina begins his day by staring longingly at a painting he has produced of a woman in a yellow dress. The woman stands on a rocky outcropping stretching out over a world of confusion. As he begins to lose himself in his creation, his alarm rings, signaling that it's time for school. As Ayato heads to school on the train with his two closest friends, Hiroko Asahina and Mamoru Torigai, his hometown of Tōkyō, the only city he knows to be in existence, is attacked by an unknown enemy.