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After the Separation of Japan in 1945, the northern island of Hokkaidō (or Ezo, as it is called in the anime) is occupied by the "Union" (referring to the Soviet Union). In 1974, the Union begins the construction of a strange tower on Hokkaido designed by a scientist named Ekusun Tsukinoe. The anime follows the story of three friends living in Aomori, in northern Japan: two boys, Hiroki Fujisawa and Takuya Shirakawa, both child prodigies; and one girl, Sayuri Sawatari. In 1996, the three are in ninth grade, their last year of middle school, and they are fascinated by the Hokkaido Tower visible across the Tsugaru Strait to the north. Sayuri becomes close friends with the two boys.
The boys find a crashed Maritime Self-Defense Force drone plane and work on rebuilding the plane with the support of Mr. Okabe, their boss at a military plant. The three teenagers promise to one day fly to Hokkaido to visit the Tower. However, before they can do this, Sayuri mysteriously disappears during the summer.
Three years later, Takuya and Hiroki have stopped working on the plane, having taken different paths after the grief they suffered at Sayuri's disappearance. Takuya is working as a physicist at an Alliance scientific facility sponsored by the United States' National Security Agency, researching parallel universes alongside Ms. Maki Kasahara under the supervision of Professor Tomizawa. They know that the Hokkaido Tower, which began operating in 1996, replaces matter around it with matter from other universes, but they do not yet know why it does this for only a 2-km radius. Takuya becomes involved with the Uilta Liberation Front after he learns that Mr. Okabe is its leader; his factory workers are the other agents of the organization. Okabe signs Takuya on for an excursion to Ezo with Uilta.
Sayuri is revealed to have been hospitalized over the past three years, having developed an extreme form of narcolepsy; she has been sleeping continuously for most of the three years. Her mind is trapped in an unpopulated parallel universe, where she is all alone. Tomizawa has discovered that she is somehow connected to the Union's research into parallel universes and the Hokkaido Tower's ability to change the surrounding land into alternate possibilities, but Tomizawa keeps this information, as well as her whereabouts, secret from Takuya initially. Tomizawa is secretly working with the Uilta Liberation Front and lets Mr. Okabe know about Sayuri, while Mr. Okabe reveals that the Uilta Liberation Front plans to bomb the Hokkaido Tower to incite war against the Union, hoping that this will lead to the reunification of Japan.
Takuya finally learns of the most likely scenario through his coworker – that Sayuri was used by her grandfather, a Union physicist, to channel all of the Tower's unstable dimension-creating energy somewhere other than Earth, the implication of him not having done so likely having resulted in the dimension creating chain reactions around the tower to continue growing in area until it enveloped the whole world. Saddened, he goes back to the old warehouse where he and Hiroki were working on the plane, only to find Hiroki, who wants Takuya to help him complete the plane to save Sayuri. He coldly points a gun at Hiroki and has him choose between Sayuri and the World without waiting for an answer – walking away in pain.
With Okabe's guidance, Takuya locks up his coworker and takes Sayuri away from the NSA compound – Takuya and Hiroki finally come back together to work on the plane. Takuya helps to finish the final programming of the plane, as they plan, using the cover of the soon coming declaration of war against Ezo, to fly to the tower and destroy it before its rays affect everything on Earth, which in turn will save Sayuri.
The plane only seats two, so Takuya allows Hiroki to pilot the plane and fulfill their childhood promise. Hiroki manages to fly the plane across the strait to the Tower carrying Sayuri and a missile provided by the Uilta Liberation Front. When Sayuri finally awakens while the plane circles the Tower, the Tower activates and immediately begins to transform the surrounding area; the area under transformation grows to encompass much of Hokkaido. In the last few minutes of her coma, Sayuri realizes that when she awakes she will lose all her memories of her dreams of the past 3 years, and thus upon waking she weeps because, unknowingly, she lost the memory of her love for Hiroki. Flying back, Hiroki fires the missile, destroying the Tower and stopping the matter transformation. The film ends with Hiroki vowing to Sayuri that they will start their relationship anew.
