The story takes place in Academy City, a sprawling metropolis where supernatural abilities have been scientifically recognized and developed. Beneath the city's peaceful facade lies its Dark Side, a hidden world of covert operations and deniable missions that cannot be made public. One of the most elite units operating in this shadowy realm is ITEM, a small team composed of four powerful girls who live and work in this dangerous environment.

Leading ITEM is Mugino Shizuri, one of only seven Level 5 espers in Academy City, whose destructive power makes her a force to be reckoned with. The team also includes Takitsubo Rikou, who possesses the rare ability to read and track the AIM diffusion fields emitted by other espers, allowing her to locate targets with precision. Frenda Seivelun specializes in combat using explosives and traps, bringing a creative and ruthless approach to their missions. Kinuhata Saiai rounds out the group, able to manipulate nitrogen at will to create a defensive shield around herself, making her the team's protector.

The narrative follows these four girls as they operate freely in the darkness, taking on assignments that range from assassinations to sabotage, always quietly setting their sights on their targets. This is a story of encounters, friendship, and the creeping darkness that surrounds them. The plot eventually builds toward a terrible incident that threatens to consume them all.

The story explores several notable arcs, beginning with the Enemy Item Arc, where a newcomer named Hanano Choubi infiltrates ITEM. Her presence sets off a chain of events involving a secret underground entertainment arena known as the Colosseum, where espers fight to the death for massive rewards, with a grand prize of 15 billion yen at stake. The team launches a bold operation to storm the Colosseum, but the path is guarded by heavy security and tightly sealed information. This arc sees the group moving through various locations, including School District 3, where they visit an insurance company's headquarters to gather information on Colosseum payments, intercept a target at the district's bus terminal, and maintain a secret base in a construction company headquarters. These events unfold in July, one year before the main story of A Certain Magical Index, showing the bonds and betrayals that shaped ITEM.