Cencoroll takes place in a Japanese city where a massive, unidentified creature suddenly appears, prompting a military response from the Japan Self-Defense Forces. Teenager Yuki, who possesses a secret potentially connected to the monster, is initially overlooked. Her friend Tetsu has been caring for a creature called Cenco, which exhibits unusual abilities. The arrival of a stranger linked to the attacking creature reveals a connection to Tetsu's pet and sets the stage for a confrontation.