The Tree of Genesis, which controls the power of creation, and the Tree of Exodus, which controls the power of destruction. Hakaze Kusaribe, a princess from a clan of sorcerers protected by the Tree of Genesis - who is also known as the most powerful of all mages - has been stuffed into a barrel and left stranded on a deserted island far off in the sea by her kinsman, Samon. Meanwhile, high school student Yoshino Takigawa meets a mysterious woman in pursuit of his close friend, Mahiro Fuwa, who disappeared one month ago. In order to avenge his younger sister's murder by an unknown suspect, Mahiro has made "a certain deal" with the sorceress Hakaze...

Samon and the rest of the Kusaribe clan have caused the Fruit of Exodus to emerge. It is said that when all of these fruits appear, the Tree of Exodus will be resurrected, and the world will end. In order to stop the clan, Hakaze communicates from the deserted island with Mahiro, using a magic doll to instruct him on how to find the Tree of Exodus, based on the direction of the fruit's flight. While seeking clues about the person who murdered his sister, Mahiro heads to his family's home - the scene of the murder - accompanied by Yoshino. The new fact that comes to light there is beyond their imagination.

In the city, now reduced to ruins, Mahiro confronts Natsumura Kusaribe, a member of the Kusaribe clan who works under Samon. Natsumura makes full use of his spear and magic as he attacks, whereas Mahiro remains on the defensive. Just then, Yoshino, whom he'd just parted with, appears before Mahiro. Mahiro, struggling in combat against Natsumura, the most skilled fighter in the Kusaribe clan, and Yoshino, racking his brain for a way to overcome Natsumura while learning how to use the Kusaribe clan's magic from Hakaze... what action did the two take...?

Somehow, Yoshino and Mahiro manage to shake Natsumura off their trail. In order to retrieve a talisman hidden by Hakaze, they visit a shrine near a mountain village. But Samon, who feared Hakaze's return, has expedited the ceremony and coincidentally, a fruit near the mountain village awakens. Thanks to the power of the talisman, Yoshino and Mahiro avoid succumbing to the Black Iron Syndrome, and they end up spending the night in the village as rain falls. As Yoshino and Mahiro takes a brief rest in a deserted house, Hakaze asks Yoshino about how he and Mahiro met.

Hakaze, guided by the direction of the flight of the Fruit of Exodus, is gradually zeroing in on the location where Samon is performing his ritual, whereas Samon is acutely aware that Hakaze is getting inexorably closer. Under Hakaze's instructions, Yoshino and Mahiro stop by a certain aquarium in order to retrieve another talisman. But again, one of Samon's subordinates, Tetsuma Kusaribe - who is also searching for Hakaze's talismans - stands in their way. Greatly outnumbered by Tetsuma and his henchmen, who soon give chase, Yoshino is struck by a memory of a day he spent with Aika at the aquarium.

What Junichiro told them was altogether too hard to believe. According to him, Hakaze's corpse had long been reduced to bones on the deserted island and has already been retrieved. Junichiro is adamant that it was Hakaze's skull, beyond the shadow of a doubt. Yoshino and Mahiro, stirred up from this shocking fact and equipped with their specially-made talismans, now have a new mystery to ponder. But instead, they decide to head for the shore near Mt. Fuji, where Samon is said to be performing the ceremony. On the way, as they set up camp, a mysterious group launches an attack on them...

Yoshino and Mahiro are walking towards the foot of the mountain where Samon and other members of the Kusaribe clan are performing the ceremony. To survive the cold, they spend the night in an abandoned bus in a scrap yard on the mountain, but Yoshino finds himself rendered speechless by his own careless words: "When it's all over..." Unable to respond to Mahiro's questions, Yoshino's mind is filled with memories of the days he spent with Aika.

As the National Defense Army launches an attack - calling it a tactical drill - on the Kusaribe clan and the Tree of Exodus, Yoshino and Mahiro, armed with the "Special Talisman" given to them by Junichiro, quietly infiltrate the area at the foot of Mt. Fuji, where Samon and the others are performing the ceremony. After they breach the barrier, they find Samon Kusaribe and a single barrel waiting for them. Samon and Hakaze begin a verbal battle, and as they remain deadlocked, Yoshino and Mahiro learn of an unexpected fact about the Tree of Genesis...

Hakaze had died "two years ago" - a fact conveyed by Samon that is altogether too difficult to believe. Learning that they'd been communicating with Hakaze while transcending time and space, Yoshino is visibly shaken, whereas Mahiro, talisman in hand, edges closer to Samon as if nothing had happened. Just as Yoshino is about to give up on everything, he remembers a certain story that Aika once told him. It is called The Tempest...

Yoshino announces that they must prepare to prove that they can resurrect Hakaze, said to be living two years in the past. To convince Mahiro that they should side with Hakaze, he also offers an unexpected incentive - that he'll reveal who Aika's boyfriend was. Mahiro decides to take the deal. Hakaze and Samon are both stunned by the fact that the mere word "boyfriend" has reversed the situation, but Samon asserts that there's no way to breach the absolute time prison. And so, Yoshino begins to prove his theory...

Yoshino and Mahiro are convinced that there's a way to destroy the time prison of two years, and bring Hakaze back to the present. Having learned from Hakaze what is needed to speak through the talisman doll, Mahiro believes that it might be possible to transcend time without causing a time paradox by using Hakaze's skeleton, now in Samon's possession, to switch out just her flesh. And so Hakaze scours the island in search of a sacrifice that will activate such magic. Just then, Samon receives word from Tetsuma on the person behind Aika's murder...

Just as Hakaze was born just as the Tree of Genesis awoke, there is a "Mage of Exodus" who was born when the Tree of Exodus was about to be revived. All parties suspect that this person might be Aika's murderer. Samon is finally driven into a corner, but on the other hand, Mahiro begins to grow suspicious, now that the situation is overwhelmingly in Hakaze's favor. And Hakaze discovers the sacrifice at last, and she successfully returns to the present. But the Tree of Genesis, in response to the Tree of Exodus, has already started to awaken all over the world, and the situation is dire.

Even in a deep, solitary slumber, the dreaming Mahiro begins to look back on all that has happened. Aika's sudden, senseless murder. His own deal with Hakaze, made in order to find Aika's murderer. Meeting Yoshino in the midst of all that chaos, and setting off on a journey to get his revenge on the culprit... As he dreams, one memory after another comes back to him. Already, a month has passed since the showdown at the foot of Mt. Fuji. The world is well on its way to being "ruled over" by the Tree of Genesis.

When Mahiro awakens on the morning of New Year's Day, Samon poses an unexpected question which was "Can you kill Yoshino Takigawa?" Meanwhile, Yoshino stops by his deserted hometown with Hakaze, and is on his way to pay his respects to Aika's grave. Afterwards, Megumu Hanemura, calling himself the "Mage of Exodus" appears before them. None of them can hide their confusion at the situation they've found themselves in. What do each of them resolve to do?

Megumu Hanemura, who proclaims himself to be the "Mage of Exodus," meets Mahiro and the others. It is decided that Hanemura should prove that he is indeed the "Mage of Exodus" as they look on. Meanwhile, to prepare for the future, Yoshino and Hakaze continue their journey to discover the whereabouts of the "Fruit of Exodus." On their way, they stop at an amusement park, where Junichiro appears, leaving Hakaze with some unexpected words.

Just as predicted, part of the Tree of Genesis has been smashed to pieces by the Tree of Exodus. Ignoring the crowd of people who are dazed by this sight, Hakaze and Yoshino head for the Kusaribe village, where it is rumored that children have seen a ghost at a shrine. Hakaze deduces that they'd mistaken an intelligence agent, there to research the village, for a ghost. Meanwhile, Yamamoto, Natsumura, and the others have secretly arrived at the village, to determine whether or not Yoshino is the "one who possesses the soul of the Tree of Exodus."

With the appearance of the "Mage of Exodus," the world has once again fallen into chaos. To restore order, Hayakawa is summoned back to government headquarters. Around that time, Hanemura, along with Yamamoto and Natsumura, is rushing to destroy parts of the Tree of Exodus, found all over the world. Meanwhile, Hakaze, still traveling with Yoshino, has been wondering whether she should forget about her romantic feelings for Yoshino, when it strikes her that she should ask him directly about the "girlfriend" he seems to cherish...

"Isn't it possible that Yoshino Takigawa's girlfriend was Aika Fuwa?"...Mahiro and the others have arrived at this possibility. It is then that Yoshino reveals to Hakaze that he was Aika's boyfriend. Despite having lost his girlfriend so senselessly, Yoshino, unlike Mahiro, has never revealed his desire for revenge, nor his hatred or rage, towards the murderer. Hakaze urges him to be more honest about what he wants. Hearing this, Yoshino bares all his hidden feelings to her as if the floodgates have been opened.

Following the "Mage of Exodus," Hakaze takes on a new role as a magician known as the "Dancing Princess," and people are thrown into further chaos. Joining Yamamoto, Hakaze learns of her theory that the "Tree of Genesis" and the "Tree of Exodus" might be the ultimate weapon for destroying civilization. Yoshino is on his way to see Mahiro, so that he can fulfill his promise of revealing who Aika's boyfriend was. Meanwhile, Mahiro is filled with the same thoughts, and the two are finally reunited at the cemetery, where they have accidentally run into each other.

Everyone is shaken when Hakaze tells them that she'd like to return to the past. She says that she must go back in order to be present at the scene of Aika's murder before she is killed, and so discover the truth about "who, how, and why" of the murder. In Hakaze's mind, it is possible in magical theory to transcend time and space to go back in time, just as she'd transcended them to go into the future. And so, gathering the necessary talismans and sacrifices, she goes beyond time and space once again...

Hakaze has returned to the past in order to discover the truth about Aika Fuwa's murder. When she accidentally runs into Aika, she is told something completely unexpected. Meanwhile, back in the present without Hakaze, a "Tree of Genesis" standing more than 100km tall has appeared. Samon, Hayakawa, and Yamamoto, thinking that this could be the "Core Block" of the "Tree of Genesis," proceed to reveal its true form. Meanwhile, Hakaze and Aika are putting their heads together to figure out who the killer was.

One day, Mahiro tells Yoshino that he'll treat him to dinner, and takes him to a restaurant in a hotel. There is a young girl there; this is the day that he first met Aika. Back in the present, Hakaze relays all of the unexpected facts that she'd witnessed in the past. Yoshino and Mahiro both pretend to take in the news calmly. Mahiro says that now that he's accepted everything, he'll be happy to save the world, and heads off to destroy the "Tree of Genesis," however...

To destroy the "Tree of Genesis," Hanemura and the others are heading towards the "Pillar," only to find that Yoshino and Mahiro have both joined the Pillar assault team. Since they can't use magic, they're initially told that they'll only get in the way, but in part because the campaign was Mahiro's idea, they both head for "the center of whatever is about to happen." The time has come to unleash their strategy, and all of the stories are now coming together like pieces of a puzzle to reveal the conclusion.

Hanemura confronts the Pillar alone. Revealing its true form to be overwhelmingly huge and powerful, Hanemura struggles against it. Hakaze and the rest of the Kusaribe clan are trying to protect the naval escort ships, only to be fired upon instead, leaving them gravely wounded at one point. Yoshino and Mahiro are watching over it all "in the center of whatever is about to happen," and it is a memory of Aika on a certain day that crosses both of their minds...