A freelance assassin known as Yuzu Tomita, a thirteen-year-old boy with an appearance so delicate he is often mistaken for a girl, receives a cryptic new order: kill the person he is about to meet. When the target arrives, it is a person who looks exactly like him, an apparent doppelgänger from a parallel world. Unable to defeat his copy in their evenly matched confrontation, the two instead demonstrate remarkable teamwork. Their handler, Yuki Komatani, accepts them both into the corporation, an underground guild of contract killers, and gives them names to tell them apart: Tomita-kun for the original and Yuzu for the copy. To maintain their cover, Yuzu enrolls in school as Tomita-kun's twin sister, Yuzuko, and the pair become known as the infamous twin assassins, Hits.

The series follows the pair as Komatani pushes them to rise through the ranks of the corporation for his own undisclosed reasons. Their days are filled with violent and bizarre assassination contracts, all while navigating the absurdities of school life. The arrival of new characters adds to the chaos, including a rising actress named Tokiyo Karasumi, who develops a serious crush on Yuzu, and teams of rival assassins sent to eliminate them. In one notable narrative arc, the school festival arrives, and Hits is tasked with putting on a play for their class project. However, their school life is further disrupted when four assassins known as the Nakamori Four Brothers transfer to their school with the explicit goal of taking their lives.

The main characters are defined by their unusual relationships. Yuzu Tomita, the original, is an accomplished and ruthless killer who develops a romantic interest in his handler, Komatani. His doppelgänger, Yuzu (or Yuzuko), shares his skills but falls in love with Tokiyo Karasumi instead. Yuki Komatani is the handsome and capable handler who serves as a foster father figure to the pair, manipulating them for his own agenda. The story is an adult-oriented action comedy, mixing graphic violence and dark subject matter with a surreal and often ridiculous tone, leading to comparisons with works known for their inventive chaos.