The young boy, Sorata Suzuhara, gets warped back in time after hearing a strange song in his field trip at the museum. As a studious and resourceful boy, he attempts to find his way back. He finds a mysterious spirit-like girl but she disappears, and for some reason feels particularly nostalgic to him and is a presence unknown to the others.

As the girls take a bath together at night, they each reflect on their own troubles, sighing. Itsuki, in the men's bath next door, lets a chick servant pass them a ladder lottery to pick a slip for a little game at night, hoping to cheer them up.

It turns out everyone had that same dream that night. Akito promises Nanami that although he hates her for taking away a precious memory from him, he doesn't want to kill her. Kakeru and Koharu are embarrassed but continue their friendship, and awkward silence ensues between Mikoto and Sakuya. Masamune further investigates the traitor in their midst after hearing of Kakeru's ear cuff going missing, touching his bed and using his ability to look into the past, seeing the shadowed face of a man. Soon after breakfast, an explosion goes off, but Mikoto's barrier isn't broken so she rushes to catch the traitor, getting knocked out by him. Sakuya, noticing her running off, dashes after her in worry but can't find her. In desperation, he uses his fragile and accidental ability to see the future, and the spirit-like girl grants his wish to use it out of his own free will for once. Although he finds Mikoto in the lodge, he ends up injured and unconscious protecting her. Koharu and Kakeru, arriving just after the traitor dashes off, bring the pair to the house.

Sorata starts to accept living on Norn9 with the teenagers, although he still intends to return home. However, as the explosion had destroyed the water supply and sewage systems, Masamune has been forced to shift it to the ship's central shaft device instead, and make a forced landing just in case. In nine days, they will reach their destinations and separate for good. Heishi resolves to make more memories with his friends, declaring that they will do a dare together. Splitting into groups, Akito, Nanami and himself head to town to first get supplies while Koharu, Kakeru, Senri and Sorata enter an old, collapsed building on the ship. Koharu notices Kakeru isn't wearing the ear cuff, but Kakeru says that's because she's around and it makes him feel safe. Meanwhile, despite her injuries haven't completely healed yet Mikoto sets about making new barriers for the structures around the ship but Sakuya drags her to his room and confronts her about the dream, making Mikoto realise her mistake. At town, Heishi gets lost so Akito and Nanami try to find him. After Akito saves her from some burly men, she recalls how she used her ability to erased his memories of his older brother, someone that he really loved and looked up to a lot. Everyone, completing their preparations, head to the old house to begin their dare, where they have to enter in pairs and make it out. Senri, Koharu's partner for the dare, is scared away by Kakeru dressing up as a monster, and the two share a kiss. Akito admits he likes Nanami, and Mikoto and Sakuya reconcile.

Morning arrives and Heishi desperately tries to contact Mikoto with his telepathy, but to no avail. Luckily, the presence of the barrier proves that she is still alive, and Kakeru finds her scarf tangled in a ladder, allowing Masamune uses his ability. They start a search for her kidnapped location on the mainland. Meanwhile, Mikoto encounters Natsuhiko and his partner Setsu Takishima that attacked the ship previously using an aircraft. Natsuhiko explains of their enemy, Shiro Yuiga, a scientist and weapon dealer that caused numerous wars over the world and wants the year 2056 to arrive. History has repeated itself many times over the course of humanity, and now they are currently living in the fourth history, with Sorata a survivor from the third history. This repeating course of history is due to the Reset, a phenomenon that ability-users can make happen. As wars start to break out all over the world, Koharu gets separated after Kakeru goes down a deserted alleyway to find Ron and meets Shiro, the man who gave her her directions to get on Norn9 and whom she nicknamed "the Traveler". Kakeru is let in on his father Shiro being alive and starts a frantic search for Koharu. He spots her distantly, but, manipulated by Shiro, she sets fire rampant on the city and force all the teenagers to retreat back to the ship.

Just as Sakuya comes to rescue Mikoto, Natsuhiko saves her from a robot attack and is gravely injured. As he undergoes recovery, The World informs the ability-users that their decision awaits them tomorrow. If they choose to initiate Reset their powers will be returned to Aion. However, because its powers are deteriorating there might be some side effects, like losing one another and their own memories. Kakeru vows never to forget Koharu. Everyone spends their last day together laughing and sharing sides of their own personality. Instead of next afternoon though, Reset initiates late at night. The teenagers' powers are absorbed into The World's Tower, which sends a burst of powerful energy connecting to Norn9. Travelling around the world, Norn9 gathers the powers from every ability-user to rewrite the world, destroying it completely, and wiping the memories of every human on Earth. Aion lets out its last song before all the forces combine, ravaging the planet.

Watching a future without Kakeru, Koharu breaks down in tears and rejects the Reset, causing her fire manipulating skills to go out of control. Everyone wakes up from their slumber, thinking the Reset has been initiated, but Masamune finds that it was just a message from Aion to test their decision. As the energy flow from The World's Tower to Norn9 has been reversed, the entire island is falling apart. Heishi telepathically tells Koharu and Kakeru to evacuate as Kakeru claws through the mountains of flames. In the end, Kakeru makes a choice to walk towards the future with her instead of living in one created by other people, and the two share a kiss, breaking the Reset. Sorata vows to stay by Aine's side after learning how she protected him for 200 years in a cold sleep to keep him alive. The ship collapses and the rest of the teenagers fly off in Norn9's extra, tinier capsules, attempting to rescue Koharu and Kakeru as the two free fall through the sky. The pressure of the wind pulls them away, and lastly, Kakeru chooses to let go just as the ship explodes. Aine, choosing free will of love for Sorata, lets him go at the same moment and tells him to live in the "true future".