The story follows Mamoru, a young boy who, after a near-death experience at age five, gains memories of a past life as an ordinary man who died alone. This revelation shatters his perception of his current world, which he discovers is filled with individuals possessing extraordinary physical abilities and a mysterious power called "Soul." His family, particularly his mother, is part of an unusual clan that enforces rigorous training on him, believing it's necessary to "wear a fitting Soul." Mamoru, terrified of death after experiencing it in his past life, vehemently refuses the training, fearing it will lead him into a life of constant battle. This refusal causes severe rifts within his family, leading to his parents' divorce and Mamoru leaving with his father.
They move to a new town, Otamachi, where Mamoru is expected to attend elementary school. His father, feeling responsible for the family's breakdown, tries to comfort him and gives him a "Soul Shooter" named "Peace Moon," a toy resembling a popular marble-shooting toy from his past life. To Mamoru's shock, Otamachi is obsessed with "Shooter Battles," with dedicated "Battle Domes" and a thriving culture around these competitions. He witnesses a junior championship match, where children, transformed into "Soul bodies," shoot glowing orbs at each other, revealing the world's true nature as a hobby-anime-like setting where toys and battles are central.
Despite his initial horror and desire to avoid Shooter Battles, Mamoru is relentlessly pursued by Sora, a classmate who wants to be his friend and battle partner. He gets drawn into a conflict with the "BB Dan," an evil organization that steals Soul Shooters and causes chaos. He reluctantly joins forces with Sora, Kai, and Rikku to form the "Mitama Shooters," fighting to protect Otamachi. During a climactic battle against the BB Dan's leader, Dr. Tamatsukuri, and his brainwashed brother Minato, Mamoru is severely injured.
Mamoru recovers and, after a year of intense battles, prepares to move again. He bids farewell to his friends, having grown somewhat attached to them and the town. His father reveals that his mother's family were guardians who used "Soul Gear" to protect people from evil, but Mamoru is now free from that duty.
Mamoru's journey continues to new towns, each with its own unique Soul Gear culture and challenges. In Kaiten Town, he becomes the reluctant leader of the "Kaiten Spinners," a team of talented but volatile young spinners who fight against the "SS Dan." He uses his past life knowledge and strategic mind to guide them, often finding himself in dangerous situations despite his desire for peace. He also encounters the "Venus Guardians," former SS Dan members who have reformed and are allied with him.
His final destination is Maishikimachi, where he is introduced to "Soul Runners." He is also accompanied by Yupiteru, a mysterious entity connected to Yukiteru, a boy with immense Soul potential whom Mamoru decides to train. Mamoru's father, seemingly aware of Mamoru's unique nature and past life, facilitates his moves and provides him with new Soul Gear, hinting at a deeper purpose and a destiny tied to his Soul. The narrative concludes with Mamoru facing a new challenge in Maishikimachi, where he must navigate the world of Soul Runners and his own evolving role, all while seeking a way to achieve his ultimate goal of eternal safety and security.