"Aria the Scarlet Ammo" is set in a world where elite schools train students in specialized combat skills. The narrative centers on Kinji Tooyama, a seemingly ordinary high school student at Butei High, an institution dedicated to training "Butei," or armed detectives. Kinji possesses a hidden ability called the "Hysteria Mode," which activates under extreme stress, granting him heightened combat skills and reflexes. Despite his potential, Kinji strives to live a quiet life, avoiding the dangers associated with his Butei training.

The story takes a dramatic turn when Kinji encounters Aria H. Kanzaki, a skilled and headstrong S-Rank Butei from England. Aria, known as the "Scarlet Ammo" due to her proficiency with dual pistols, becomes Kinji's partner after a series of events forces them to work together. Their partnership is initially rocky, as Aria's fiery personality clashes with Kinji's desire for a peaceful life. However, as they face increasingly dangerous missions, their bond deepens, and Kinji's Hysteria Mode becomes a crucial asset in their battles.

The plot unfolds through a series of missions and investigations, often involving criminal organizations and rival Butei. Aria and Kinji are frequently pitted against powerful adversaries, including the enigmatic organization known as "E.U.," which seeks to destabilize the Butei system. Alongside Aria, Kinji interacts with other key characters, such as Riko Mine, a tech-savvy Butei, and Shirayuki Hotogi, a swordswoman with a deep loyalty to Kinji. These relationships add layers to the narrative, exploring themes of trust, loyalty, and the moral complexities of their roles as Butei.

As the series progresses, Kinji's past and the origins of his Hysteria Mode are gradually revealed, tying into the larger conflicts within the Butei world. The story balances action-packed sequences with moments of character development, particularly in Kinji's struggle to reconcile his desire for normalcy with his growing responsibilities as a Butei. Aria's determination to prove herself as a top Butei and her evolving relationship with Kinji serve as central emotional arcs, driving the narrative forward.

The series concludes with a climactic confrontation against the forces threatening the Butei system, testing the limits of Kinji and Aria's partnership. While the resolution ties up major plot threads, it leaves room for further exploration of the characters' futures, reflecting the ongoing challenges of their lives as Butei.