Kenshi is a troubled boy, who had been repeatedly tormented by a couple of bullies in a public restroom within their school. Although he was saved from humiliation by a girl named Aiko Sasahara, they continue their activities with him and decided to leave him within the confines of an emergency safety house. He had a long history of being bullied due to his mother being "strange", and along with her, he was badly ridiculed for this. When his mother died, he was so stricken with grief that even into his teens, he wished he had died with her. His emotional torment continues, and which at the same time the monster begins to come to surface within Tagruato's oceans. He later escapes the school grounds with Aiko's help to his house after seeing news coverage about the monster. Here, the two bond together while on their way to Kishin's apartment to seek shelter, only to stumble across an unknown cult bent on using him for a dark purpose tied to the monster. Unlike his mother, Kishin and his father are not on good terms as seen in some panels.
Medical records seen at his father's room, along with the cult tracking him down, heavily implies that Kishin is part of a series of experiments with an item revered by the cult, that ties him to the monster itself. In the third chapter, it is seen that his system has been mixed with the monster's own stimuli made into a tiny organ called the Splinter of Amnion to allow him to control it without him falling to its wrath. Kishin's father confirms this as an act of sabotage by his mother, whereby she used Kishin as a vessel under the cult's orders, but dies by Tagruato's hands.
Kishin succumbs to madness due to the betrayal of his mother and now uses the monster to cause more destruction. He is able to control the monster without it harming him, it thinking that the child is its kin or brethren. In the final chapter, with the help of Aiko, Kishin gains his sanity back, learns to value the life of others and his own and faces the monster, where it removes the Splinter of Amnion from his system to its own, but it cannot feed on the emotions Kishin has laced it with, it leaves Kishin in the seas of Japan where he is rescued by Aiko and the bullies. The manga ends as they embrace, having finally found the one thing he cares for in his life.