Four years ago, a "Gate" to another world suddenly appeared in Mikado City, and invaders known as Neighbors, 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. Presently, 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 the strange Yuma, who knows nothing of Japanese common sense and remains unharmed even after being hit by a bicycle. After school, Yuma is taken to the old forbidden zone by delinquents, and Osamu follows to try and save him. During this, a Gate opens behind the school—which was supposed to be safe—and an insect-type Trion Soldier, Marmod, 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 destroys 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 in his report to HQ, saying "I defeated the enemy myself" to protect Yuma. Yuma also recognizes Osamu's sense of justice—trying to protect others even when his power falls short—and takes an interest in him. Thus, the Border agent and the humanoid Neighbor, two beings who should never have associated, begin to build a strange relationship of trust. Meanwhile, HQ begins investigating the unidentified Black Trigger reaction, and the top brass and A-rank agents grow increasingly wary of the presence 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.