In the distant future, human beings have been forced to leave earth and migrate to another galaxy. An advanced team of spacecraft arrives at a planet that is to be terraformed. Each member of the team is output by a biological 3D printer.

Tsutomu, an average middle school kid busy studying for the final exams to enter high school runs into a man running from someone and gets caught up in the chase. In all the confusion he gets accidentally killed. Luckily Birdy (an interplanetary agent) knows a way to save him, unfortunately that means joining bodies to become one. So now he is stuck with this officer and along for the ride capturing criminals and saving lives.

After fending off the threat of a Neuroi invasion of Romagna and destroying the enemy's nest over Venezia, Yoshika Miyafuji goes back to her home town in the Empire of Fusou. Despite the loss of her magical and healing abilities, the former officer of the 501st Joint Fighter Wing wants to continue studying medicine. This is in order to help those in need, both civilians and those on the front lines alike. She receives an invitation from a prestigious school in Europe and decides to accept the offer, embarking on a journey back to the war-torn continent. However, a new danger arises, as more and more Neuroi manage to break through human defense lines, appearing unnoticed in supposedly safe areas and disturbing the balance of power in Europe. Yoshiki's sense of duty collides with her inability to pilot a Striker Unit, but with her friends in peril, it seems that there is only one thing she can do.

All hope seems lost when the world is suddenly invaded by aliens. Earth's only defense is a small three-person team known as the Special Counter-Aliens Task Force, consisting of an anonymous director, the tyrannical Shiro, and the easygoing Arikawa. The luck of the Task Force improves when Arikawa finds a teenage boy lying alone on a hill. The boy, Kakashi, is humanity's only hope—he has power previously unbeknownst capable of defeating the aliens! However, without any memories and with no knowledge on how to use his power, Kakashi is left clinging to Arikawa and Shiro as well as the only remnant of his previous life: his broken cellphone. Kakashi is conflicted by the fears and emotions clouding his mind and he calls his own motivations into question. Can he overcome his doubts and internal struggles and save the world? [Written by MAL Rewrite]