Ken Shirogane, an impetuous and courageous Earth boy, is chosen as one of five to embody reincarnated spirits of ancient Mu warriors. His human bravery enables the cyborg Madora to summon the warrior Kein's spirit into his body. Unaware of his destiny, Ken discovers a mysterious mark leading him to an island alongside Rei Shiratori, Yozuro Shiraki, Manabushi Rokawa, and Rokase Shinmu.

There, he encounters Madora and meets the spirit of King Ra-Mu. Ra-Mu explains that recent natural catastrophes herald the awakening of Atlantis, revealing Ken and the others as descendants of Mu with the declaration: "All men are children of Mu." As conflict escalates, Ken integrates Kein's identity and powers, navigating the complex interplay between his original self and the inherited warrior persona.

Gaining access to advanced technological spaceships, Ken battles resurgent Atlantean forces led by Empress Condra and the awakened Zarkon. These events coincide with the re-emergence of Mu's emblem, a colossal white whale. Ken confronts the legacy of the ancient war between Mu and Atlantis, which devastated both civilizations 30,000 years prior. His journey shifts him from an ordinary human to a key Earth defender, tasked with halting Atlantis's destruction.

His actions contribute to locating the pivotal Olymphalcon artifact sought by the antagonists and thwarting Zarkon's resurgence. The narrative spans Ken's initial awakening through pivotal events, including the white whale's transformation and decisive battles against Atlantis.