The world has been engulfed in a desperate, three-decade-long war against the BETA—an alien species that invaded the planet in 1973. Amid this chaos, a high school student named Takeru Shirogane suddenly wakes up from a terrifying nightmare where he sees mankind in utter defeat. Soon after, he realizes that his dream was nothing more than the recollections of his life in an alternative universe. In those memories, the Alternative V project is implemented, sending hundreds of thousands of people into space as a last resort to preserve humanity, while leaving the remaining billion on Earth to suffer a cruel fate. Yearning to change this grim future, Takeru joins a military base in Yokohama, which happens to be his former high school. There, he manages to convince the base's vice-commander and leader of the Alternative IV project, Professor Yuuko Kouzuki, to prevent Alternative V from happening. To ensure the success of Alternative IV, Takeru must pilot the gigantic humanoid machines Tactical Surface Fighters (TSF) alongside his fellow cadets. However, he has only two months to complete his training and exploit his partial knowledge of the future—lest the ensuing tragedy take place.

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.