A world where it has been established that people routinely swing between slightly different parallel worlds... Koyomi Hidaka, who lives with his father following his parents' divorce, meets a girl named Shiori Satou at the research institute where his father works. They both have a little crush on each other, but everything changes when their parents remarry. Koyomi and Shiori, convinced that they will never be together, try to jump into another world where they won't be step-siblings... There's no meaning in a world without her.

In a tranquil neighborhood of Tokyo, seven students are avoiding going to school—hiding in their darkened bedrooms, unable to face their family and friends—until the moment they find the mirrors in their bedrooms are shining. At a single touch, they are pulled from their lonely lives into a wondrous castle straight out of a Grimm's fairy tale. This whimsical place, oddly lacking in food and running water but full of electrical sockets, is home to a petulant girl in a mask, named Wolf Queen and becomes their playground and refuge during school hours. Hidden within the walls, they're told there's a key that will grant one wish, as well as a set of clues to find it. But there's a catch: the key must be found by the end of the school year and they must leave the premises by five o'clock each day or else suffer a fatal end. As time passes, a devastating truth emerges: only those brave enough to share their stories will be saved. And so they begin to unlock each other's stories: how a boy is showered with more gadgets than love; how another suffers a painful and unexplained rejection, and how a girl lives in fear of her predatory stepfather. As they struggle to abide by the rules of the game, a moving story unfolds, of seven characters trapped in a cycle of misunderstanding and loneliness, who are ultimately set free by the power of friendship, empathy, and sacrifice.

In 2038, Yuuma Sawatari is an elementary school kid who loves everything about space and astronomy. He was initially excited when his parents bought a robot called Nanako, but he was disappointed when he learned that she was basically just a boring housekeeping robot. However, when he does finally try to talk to her about space, something strange happens. Her system crashes and is taken over by what claims to be a marooned alien ship! The alien ship wants Yuuma's help to get back to space!

Thanks to Professor Yuuko Kouzuki's technology and Kasumi Yashiro's psychic powers, Cadet Takeru Shirogane travels back to his original world. With no time to lose, Takeru aims to enlist Yuuko's help in his world to complete the Alternative IV project—the last hope humanity has against the BETA, an alien species invading the planet. As the anti-BETA project nears completion, Takeru and other cadets graduate from the Yokohama pilot training academy. However, during a test of the new operating system for the Tactical Surface Fighters—the giant combat suits used by humanity against their adversary—the BETA ambush Takeru and his team. Barely escaping with his life, Takeru is left traumatized after witnessing the cruel death of one of his close friends. Losing his will to fight, Takeru flees back to the other world, where he experiences a similar tragedy. According to Yuuko's theory, people from parallel universes are bound to suffer the same fate. As a result, Takeru must overcome his trauma if he wants to protect the ones he holds dear.