A gate to another world once opened in the peaceful Japanese city of Mikado City, unleashing interdimensional invaders known as Neighbors. Conventional weapons proved useless against them, but a mysterious organization called the Border Defense Agency fought back using specialized weapons called Triggers, which convert a user's life energy, or Trion, into combat abilities. Four years later, Border has built a massive base and stands as humanity's shield, though the threat of Neighbor attacks remains constant.

Osamu Mikumo is a low-ranking Border agent with very little Trion but a strong sense of justice. His life changes when he meets a new transfer student at school, Yuma Kuga. After defending Yuma from bullies, Osamu finds himself caught in a Neighbor attack. When Osamu struggles to fight the invader with his own Trigger, Yuma steps in and defeats the creature with astonishing ease, using a unique and impossibly powerful weapon called a Black Trigger. Osamu soon learns the truth: Yuma himself is a Neighbor from the other dimension, known as the Neighbourhood, and the Black Trigger he possesses is a legendary artifact created from his own father's life. Their encounter sets in motion a conflict over the power of the Black Trigger, drawing the attention of Border's elite operatives and enemy forces alike.

Yuma joins Border alongside Osamu, as well as their friend Chika Amatori, a young girl with massive Trion reserves who is hesitant to fight. The story follows the trio as they train, participate in rank wars against other Border squads, and face escalating threats including a massive coordinated Neighbor invasion of Mikado City. The reboot project covers the narrative from the very beginning, including the Black Trigger capture arc that introduces Yuma and Osamu's partnership, the Border Enlistment arc, the Large Scale Invasion arc where the city faces its greatest crisis, and the B Rank Wars arc focused on team battles and strategy.