Kinnikuman II Sei takes place several years after the events of the original Kinnikuman. Mantarou Kinniku is the 59th prince of Planet Kinniku and son of the renowned wrestler, King Suguru. Lazy, immature, and cowardly, Mantarou seems to have little in common with his heroic father. When a powerful group calling themselves the dMP threatens the Earth, only someone as powerful as Kinnikuman stands a chance against them. Not knowing the current whereabouts of the King, a plan is formed to have his son Mantarou take up the mantle. The idea of fighting super villains does not sit well with Mantarou, who initially runs away from his duty. He flees to Earth where he encounters Meat, his father’s old trainer. Despite Mantarou's shortcomings, Meat sees King Suguru in him, and believes he can set the prince on the right path. Thus begins Mantarou's journey to better himself and save the world.

The Chojin Crown, the tournament which Mantaro (Kid Muscle) reluctantly participates in. After going along with the obstacles (most of which were created to try and eliminate him), he qualified.

Tired of writing riddles for children, Yamaoka Momosuke plans on gathering spooky and gruesome stories and publishing them in an anthology called Hyakumonogatari ("One Hundred Tales"). While researching these old myths and legends he comes across a mysterious trio who call themselves the Ongyou. They are detectives who are investigating the legends to reveal their truths...and bring those in the wrong to justice. Each time Momosuke meets the Ongyou he must face horrible truths and battle with his morals, but he's seeing things he shouldn't be seeing...