Hayato Arashiyama lives peacefully with his adoptive parents and pet dog Jack until a giant robot called Golem attacks his city, killing his parents amid widespread destruction. In his father's dying moments, Hayato learns he was adopted after being found ashore from a shipwreck—a revelation central to his identity. Orphaned, he is taken in by industrialist Kuroshio, whose life Hayato and his father once saved in a car accident. While living there, Hayato discovers a hidden hangar containing the same Golem, exposing Kuroshio's involvement and a conspiracy by the Boa corporation.

Hayato's quest shifts from avenging the falsely accused Phantom Ship to uncovering Boa's operations, including its addictive soft drink, Boa Juice, which causes consumers to melt into ooze when overconsumed. During a televised interview about the Phantom Ship, he risks his life to expose Boa publicly. His investigation reveals Boa murdered his biological parents by setting their ship ablaze years earlier. Aligning with the Phantom Ship's captain—revealed as his disguised biological father—Hayato assaults Boa's undersea base. In the climax, after his father is wounded, Hayato and a young girl orphaned by Boa launch a kamikaze strike to destroy the base, though both survive.

His loyal dog Jack remains a constant emotional support throughout. Hayato evolves from a traumatized victim seeking revenge into a resolute fighter against systemic corruption, driven by the loss of both his adoptive and biological families.