Teenage assassins Mahiro and Chisato visit the coastal city of Miyazaki for a contract and a vacation when they unexpectedly cross paths with a legendary, bloodthirsty assassin who's looking to add to his kill count.

Baby Assassins is a thrilling action comedy that follows a group of high school girls in Japan who are recruited by a crime family to become assassins. The story revolves around their struggles as they balance their daily lives as students with their secret lives as killers. With a mix of martial arts action, comedy, and drama, Baby Assassins takes the audience on a wild ride filled with violence, friendship, and unexpected twists.

Chisato and Mahiro must pay four years of overdue fees or lose their membership in their assassin guild. They take part-time jobs, but find themselves in the middle of an armed robbery and being hunted by other assassins.