Medarot 5 follows the adventures of Koishimaru Tensan, who has recently moved to the small town of Susutake. Koishimaru gets a new Medarotch and meets a boy named Yamato Shijimi, but his Medarotch breaks after he gets pushed into cow manure. He later finds an abandoned Medarotch and Medarot Chrotojil inside of a tree and is forced to activate them in a sudden Robottle.