A giant monster sends a town's citizens into a panic, except for a girl named Yuki and her schoolmate Tetsu. Tetsu happens to have his own strange creature named Cenco as a pet. Another boy named Shuu controls the monster threatening the town, and the stage is set for a battle.

Student Yuki has never seen one of the giant monsters she always hears about on the news and that threaten her city. But when she meets the lethargic Tetsu one day, things change suddenly. Because Tetsu moves around the houses with a creature called Cencoroll, which he can control with mind control and which can transform into a wide variety of objects. But not only Yuki is fascinated by Cencoroll: the boy Shu tries to take Cencoroll from Tetsu with the help of his own telepathy monster, whereupon the four engage in a bitter fight, in which Yuki also intervenes and the entire city is converted into a battle arena.

Cencoroll 3 is the finale to the main characters Tetsu and Yuki's story.