In an alternate timeline, Japan was divided after losing World War II: Hokkaido was annexed by "Union" while Honshu and other southern islands were under US sovereignty. A gigantic yet mysterious tower was constructed at Hokkaido and could be seen clearly from Aomori (the northernmost prefecture of Honshu) across Tsugaru Strait. In the summer of 1996, three 9th-graders had made a promise that one day they'll build an aircraft and unravel the tower's mystery, but their project was abandoned after the girl, Sayuri Sawatari, began experiencing sleeping sickness and transferred to Tokyo for better treatment. Three years later, Hiroki Fujisawa accidentally found out that Sayuri had been in a coma since then, and he asked Takuya Shirakawa to help him finding a way to revive her. What they don't know yet is that Sayuri's unconsciousness is somehow linked with secrets of the tower and the world.

(Source: Anime News Network)