Four years ago, a "Gate" to another world suddenly appeared in Mikado City, and Neighbors—invaders immune to conventional weapons—attacked the city. On the brink of destruction, a mysterious organization called "Border" repelled the Neighbors with unknown weapons called "Triggers" and built a headquarters base. Since then, Mikado City has barely maintained peace thanks to Border. Currently, a white-haired, red-eyed transfer student named Yuma Kuga arrives in the class of Osamu Mikumo, a serious boy attending Mikado City Third Junior High. Osamu is shocked by Yuma's strange behavior, such as being uninjured after being hit by a bicycle and his lack of Japanese common sense. After school, Yuma is taken to the old forbidden zone by delinquents, and Osamu follows to help. During the confrontation, a Gate opens behind the school—a place that should be safe—and a Marmod, an insect-type Trion Soldier, appears. Osamu activates his Trigger as a Border C-rank agent to fight, but his training Trigger is no match and he is cornered. Then, Yuma reveals he is a Neighbor from beyond the Gate and activates his Black Trigger. With overwhelming power, he obliterates the Marmod in an instant, saving Osamu. After the battle, Osamu accepts the fact that his life was saved by someone who should be an enemy, and he lies to Headquarters, claiming he defeated the enemy himself to protect Yuma. Yuma, in turn, becomes interested in Osamu's sense of justice—trying to protect others even when his strength falls short. Thus, the Border agent and the humanoid Neighbor, two beings who should never have associated, begin to build a strange bond of trust. Meanwhile, Headquarters begins investigating the unidentified Black Trigger reaction, and the top brass and A-rank agents grow increasingly wary of a new humanoid Neighbor. The meeting between Osamu and Yuma is the beginning of a destiny that will eventually lead to a great war over Mikado City and the Neighborhood. And so, it begins...

The next morning. Osamu arrived at his classroom at Mikado Third Junior High at his usual time.