Haruka Mishima and Ayato Kamina were typical teen sweethearts living in Tokyo, until one day a cruel twist of circumstance separated them. Whilst Haruka was on vacation, Tokyo was closed off from the rest of the world by an Absolute Barrier created by the Mulians, beings from another dimension. Whilst fifteen years pass outside the barrier, in Tokyo time moves much more slowly, and by the time Haruka and Ayato are reunited, there is a twelve year age difference between them. Whilst keeping the truth about their shared past a secret from Ayato, Haruka brings him out of Tokyo, where he fights against the Mulians using a mysterious giant robot known as the RahXephon. But Ayato’s destiny is far more important than he first realises- for his fate, and that of the RahXephon, inextricably links the future of both humans and Mulians as he becomes the ‘tuner of the world’. But how will Ayato come to realise this fate, and what part will his continuing feelings for Haruka play in shaping events?
In the year 2012, Haruka Mishima and Ayato Kamina are teen sweethearts living in Tokyo. With each passing day, their relationship deepens, until a twist of fate pulls them apart. For, whilst Haruka and her family are away on their Christmas vacation, Tokyo is sealed away from the rest of the world by an Absolute Barrier created by the Mulians, beings from another dimension.
In the outside world, 15 years pass, and Tokyo–Jupiter (so called because the appearance of the barrier resembles the surface of Jupiter) remains sealed away. Outside, a group known as the Foundation plot their future plans, plans that are linked to the humans, Mulians, and to a mysterious sleeping girl called Quon.
Inside Tokyo-Jupiter, time moves more slowly, and for Ayato, only three years have passed since he last Haruka. Images of her still haunt his dreams, in some ways even more vivid than the world he inhabits, a world in which he believes the 23 million people living in Tokyo make up the entire population of the world.
One day, however, Ayato’s entire world is turned upside when the train crashes on the way to school. After running off to find help for his injured friends Asahina and Mamoru, Ayato finds himself outside, watching as military forces fight an aerial battle above the city. Ayato looks on in surprise and confusion, until he is distracted by a vision of Haruka, just as he remembers her.
Following the vision, Ayato goes into a nearby station, only to be intercepted by a pair of armed men, who claim they have been sent by his mother, Mayaa. Whilst Ayato tries to figure out just what is going on, a mysterious woman attacks the two men and incapacitates them. Ayato is mystified even further to note that the men have blue blood, but the woman promises that she will explain everything if he comes with her. Ayato is understandably reluctant to go with her, and so she is forced to inject him with a substance that renders him unconscious.
What Ayato doesn’t realise is that the woman is none other than his beloved Haruka Mishima, who, thanks to the time difference, is now twelve years older than him. However, Haruka now uses a different surname, Shitow, and for now she has deemed it best not to tell him who she is.
Some hours later, Ayato finally comes to in Haruka’s car. Once again promising to tell him the truth, Haruka stops off at a hangar, and they board a two person aircraft. Haruka tells them that they will be leaving Tokyo, but once in the air, she finds herself unable to control the craft. She is inexorably taken back inside the city, to a shrine owned by the Mulians and under the jurisdiction of their leader- Ayato’s mother Maya.
As they approach the shrine, Ayato ejects from the aircraft, and heads for the central area where the giant robot known as the RahXephon awaits. Under Ayato’s control, the RahXephon awakens, enabling him to pick up Haruka, fight off the Mulian Dolems (giant remote-controlled weapons) and make his escape, leaping right past the Absolute Barrier. With blue blood streaming from a cut in her face, Maya calmly watches her son leave- he will return to her soon enough.
Awakening once again, Ayato finds himself outside the barrier, and, contrary to what he has been told, the outside world has not been destroyed. But there is one more surprise in store for him, as Haruka finally explains about the time difference between Tokyo and the rest of the world.
Soon after, Ayato and Haruka are picked up by TERRA, the anit-Mu organisation that Haruka works for. After being taken to TERRA’s base on Nirai Island, Ayato is immediately sequestered in a high security cell whilst doctors run tests on him. Despite Haruka’s protests, her superiors tell her that these procedures are necessary, especially given their findings- Ayato has the so-called Mu phase in his blood. Eventually, his blood will turn blue and he will turn into a Mulian- and when the time comes for him to fulfil his destiny and use the RahXephon to ‘tune the world’, the resulting reality will belong to the Mulians. Their only hope is to get Ayato to ‘tune the world’ whilst his blood remains red.
After the initial tests, Ayato is released into Haruka’s care, and she takes the opportunity to further update him on the situation. Some years ago, the Mulians began appearing on Earth, but despite initial attempts to merely fit in with human society, something happened to change that. A war between humans and Mulians began, and a full-scale conflict was only narrowly avoided fifteen years ago, when the Mulians shut themselves away behind the Tokyo Jupiter barrier. Now, there are only occasional skirmishes with the Mulians, and it almost seems as if the enemy is waiting for something.
To complete Ayato’s orientation, Haruka plans to show him the sleeping Quon, but her guardian Itsuki refuses- now is not the time. He is willing to talk about her, however, explaining that she is his Sleeping Beauty, a full-blooded Mulian destined to one day awaken and tune the world.
Convinced that his Haruka is still alive, Ayato promises to help TERRA protect humanity (and thus Haruka) from the Mulians by piloting the RahXephon. To that end, he remains on Nirai Island, living with Haruka, her little sister Megumi and their uncle Rikudoh.
The weeks come and go, and Ayato continues to fight the Mulians and their Dolems, until finally one of them gets the better of him in battle, and draws him back through the barrier. Just as Maya predicted, Ayato has returned to her.
Ayato is back in Tokyo, but everything is different now. His friend Asahina is beginning to turn into a Mulian, and as her blood turns blue and her human memories start slipping away, she become paranoid and stressed. Meanwhile, Maya explains to Ayato about the true nature of the Mulians- they are from a parallel universe, and can only exist on this world as blue-blooded humans synchronised with a Dolem.
Ayato cannot help wondering how his existence fits in with Maya’s plans, she explains that her desire to have a child has nothing to do with her role as the Mulian leader. Initially, Maya was the one destined to pilot the RahXephon, but by the time she regained her Mulian memories, she was already pregnant with Ayato. Maya chose to give birth to Ayato and raise him, but despite the strength of her love for him, her duty was unavoidably passed on to him- forcing Ayato to become the RahXephon’s pilot.
Unable to cope with any more, Ayato leaves, and at the same time the RahXephon breaks free from the shrine and heads out to his location. As Ayato makes his way to it, he runs into a scared Asahina, whose has finally been forced to let go of the illusion of a normal world after discovering that Mamoru is also a blue blooded Mulian. Taking Asahina with him, Ayato boards the RahXpehon and once again leaves Tokyo Jupiter.
Fleeing from both TERRA and the Mu, Ayato and Asahina head to a distant town, and try to set up a new life there. Ayato takes on a part-time job, and the two live together quietly for a time. Asahina is happy, but she is all too aware that it cannot last- for one thing, her human memories are fading away, and even now she can no longer remember anything about her friends and family.
Predictability, Ayato and Asahina’s time together comes to an abrupt end when a Dolem appears in the city. Realising that he wants to protect Asahina, Ayato goes out to fight the Dolem, unaware that it is actually synchronised with Asahina herself. Even as Ayato destroys the Dolem, back at their apartment, Asahina suffers the same injuries. Nonetheless, she uses the last of her strength to write a message to Ayato in her diary, and through the Dolem that message is reproduced in the lights of the city. Engrossed in the battle, Ayato initially fails to notice the message, but when the Dolem finally goes down, he catches sight of Asahina’s last words- “Ayato…Goodbye…”
Some time later, a retrieval team from TERRA finds Ayato, along with Asahina’s body. They manage to bring him in, but a scuffle over the handling of Asahina’s remains leads to an unfortunate discovery- Ayato’s blood has already turned blue.
Whilst he waits for TERRA to release him, Ayato sinks into despair- he chose to fight to protect Asahina, but even so he proved unable to save her. A concerned Haruka comes to visit him, and after an initial attempt to keep his distance, Ayato gives in when he realises the depth of her concern for him. As Haruka promises Ayato that he need no longer pilot the RahXephon if he doesn’t want to, she finds herself unable to hold out any longer. Moving closer, she kisses Ayato, and, after his initial surprise, he kisses her right back. In short order, the two are enjoying the intimacy that Haruka has waited so long to have.
Returning to life on the island, Ayato finds himself spending time with Haruka’s sister Megumi, and a casual conversation with her reveals another piece of the puzzle as he learns that Haruka Shitow was once Haruka Mishima. Confused, Ayato cannot help wondering just why Haruka chose to keep the truth a secret from him all this time.
Events continue to move forward, as TERRA’s commanders begin preparations for Operation Downfall, a plan to destroy Tokyo Jupiter’s Absolute Barrier using special resonance generators. Meanwhile, Haruka decides to pursue an inquiry of own after discovering that her uncle Rikudoh’s daughter is none other than the Mulian leader Maya Kamina. At Haruka’s insistence, Rikudoh finally reveals the truth that he kept buried for so long. Years ago, his daughter fell in love, and although the couple were still young, they conceived a child together- Ayato. Unfortunately, Maya’s blood soon turned blue, and with it all memories of her earlier life were lost. The only connection she had to those past memories was her unborn child, whom she guarded fiercely.
However, Maya’s love for a human did not fit in with the machinations of the Foundation, and so Rikudoh decided to help the young couple flee, choosing his daughter’s happiness over her role as destined pilot of the RahXephon. Shortly after, Kamina’s dead body was found, but Maya herself managed to remain hidden for another fifteen or so years, until she finally revealed herself on the day the Absolute Barrier was created.
Neither Ayato nor Haruka want the RahXephon to be piloted again, but events are moving beyond their control, and Quon’s guardian Itsuki is determined to see things run their course. He takes Ayato to see the sleeping Quon, and instructs him to wake the Sleeping Beauty with a kiss. When Ayato proves unwilling to do so, Itsuki forces him, and shortly after his lips are pressed to Quon’s, she finally awakens. Exploding out of her sleep, Quon thanks Itsuki for the care he gave her, before floating away to meet her destiny.
With Quon gone, Itsuki explains her role to Ayato. Long ago, it was she who used the RahXephon to ‘tune the world’ of the Mu, but when she failed, she, Maya, and the Foundation’s leader Bahbem were all cast out and sent to this world. Now that Quon has reawakened, fate will force her to attempt to tune the world again, but her tuning can only bring collapse and ruin. The only one who can stop Quon and tune the world correctly is Ayato himself. Desperate to see his beloved Quon saved, Itsuki begs Ayato to fulfil his destiny and pilot the RahXephon one more time. Ayato agrees- not for Itsuki, but for himself, and for the person that he wants to protect.
With their preparations complete, TERRA sets Operation Downfall in motion. As the resonators bring down the Tokyo Jupiter barrier, Commander Isshiki Makoto is delighted with his success- but just as the barrier kept humans out, it also kept the Mu in. With the barrier down, Mulian cities begin materialising all over the world.
Whilst heading to the RahXephon to perform his duty, Ayato is intercepted by Haruka. She is there to do more than say goodbye- when she first freed Ayato she promised TERRA’s commanders that she would kill him rather than let him tune the world as a Mulian, and now it seems that she has come to fulfil that promise. Beyond her duty, however, Haruka is also scared that Ayato will lose his humanity when he joins with the RahXephon again. Ayato knows that, but he also knows that he cannot delay- with the turning of his blood his memories have also begun to fade, including those of their shared past. For Ayato, it is important to do this while he still remembers Haruka and his love for her- whilst he still knows why he is fighting and what he wants to protect. And, despite her reluctance, Haruka has no choice but to let him go.
As the RahXephon takes off, Haruka collapses in tears, only to find herself back at her old middle school, confronted with a being that resembles herself. Her past self tells Haruka that she too has a role to play- for Ayato to find himself he will need a point of reference, and Haruka must be that point of reference for him. If what she wants is to be with him, then she must go to him now.
Now that they are free, the Mulians deploy the full force of their Dolems against the humans, and an intense aerial battle breaks out. In the midst of this, Ayato and the RahXephon appear, transformed into their ultimate form- the True Sacred RahXephon. In an attempt to avenge Asahina, the Mulian Mamoru sends his Dolem to attack the RahXephon, but when he rips out the pilot seat, there is no one there. Ayato has fused with the RahXephon, and as a counterattack, he tears Mamoru apart, finishing him off with a blast of sound.
As the power of the RahXephon sweeps across the battlefield, humans and Mulians alike are destroyed. But soon, an equal force rises to meet Ayato- Quon’s own RahXephon. Now, the time has come for the two to battle, and to the victor will go the task of tuning the world.
Down on Nirai Island, the inhabitants rush to evacuate, all that is, except Haruka. Even as the others leave, she flies a plane right into the middle of the RahXephon battle. The aircraft is soon destroyed, but Haruka finds herself transported to a mysterious room, where Maya Kamina awaits.
As Haruka listens, Maya explains her feelings. She wanted to be the only one that loved Ayato and was loved by him, the one that would guide him and listen to him and be his entire world. But Haruka interfered with that- she showed him a different world, and became the one Ayato loved the most. Now, Maya must accept the way things turned out, and, so saying, she sends Haruka to do what Maya herself cannot – go to Ayato and share his suffering.
Whilst the two RahXephons fight, Haruka searches for Ayato in the other world. With her feelings for him guiding her steps, Haruka is soon reunited with Ayato, but is no longer the Ayato he once was. He has become the Observer of Time, the being that must observe the world in order for it to exist in a well-defined fashion. Without an Observer, the world will dissolve into chaos and noise, and Ayato has chosen to take on this role so that this will not happen- so that there will be a world for Haruka to return to. And even though he cannot go back with her, nor choose her future, together with the spirit of the RahXephon he has the ability to give her memories of the past she has always wanted- a past in which she and Ayato were able to grow up together.
Infused by the power of Ayato and Haruka’s feelings, the RahXephon is given new strength, and back in the human world, Ayato’s RahXephon is finally ale to vanquish Quon and bring forth the tuning of the world. As the RahXephon finally taps into its full power, the world is suffused with light and sound, and soon it is transformed, not for humans or Mulians, but for all living beings.
Decades later, a teenage girl named Reika listens to her grandmother Haruka as she reads “Through the Looking Glass”. Reika wonders if the waking world in the story is any more real than Alice’s dream world, but Haruka tells her that it doesn’t matter. What are important are memories, for these are what define reality for each person- just as Grandpa Ayato always used to say. He may not be with them anymore, but Reika is well aware of just how important he was- just look at how much Haruka talks about him!
As Reika goes off to make some tea, Haruka remains outside. Looking out to see, she sees a vision of Ayato, and as he smiles at her, Haruka herself is young once again. Beyond the restraints of time, Haruka and Ayato’s love helped them to find each other, and create the reality they always wanted.