In Academy City, where supernatural abilities are a recognized science, a shadow organization operates beneath the peaceful facade. This is the Dark Side, a world of covert missions, assassinations, and secrets that never reach the public. One of its most elite units is ITEM, a four-member team of operatives who carry out the city's most dangerous and unsanctioned tasks.

The team is composed of four young women, each wielding a unique and formidable power. Shizuri Mugino, one of only seven Level 5 espers in Academy City, serves as the unit's leader and possesses overwhelming offensive capabilities. Rikou Takitsubo acts as the team's tracker, able to sense and follow the AIM diffusion fields emitted by other espers. Frenda Seivelun is a combat specialist who relies on a vast array of explosives and cunning traps. Saiai Kinuhata provides defense by manipulating nitrogen to create an impenetrable shield around herself. Together, they operate with precision and a cold efficiency, taking on missions that go far beyond the law.

The story follows ITEM as they navigate the underworld of Academy City, targeting other dark side operatives, eliminating threats, and seizing objectives for their unseen handlers. Their latest assignment, however, begins to unravel the fragile trust that holds the group together. A new variable, a fifth girl, is introduced into their ranks, an infiltration that sets the stage for a devastating incident. As the team moves through locations such as the commercial zones of School District 3 and the hidden facilities connected to the Colosseum, they find themselves caught in a conspiracy that forces them to confront the brutal reality of their existence. The bonds of friendship and survival are pushed to a breaking point, leading to a tragedy that will scar the unit and fundamentally alter their dynamic, laying the groundwork for their eventual role in the larger conflicts of Academy City.