Goh Arisaka, a young United Nations worker stationed in Antarctica, finds his life upended when mysterious black cylinders emerge from the ice. Amidst the ensuing crisis, he joins the crew of the resurrected undersea battleship Ra. There, he makes a shattering discovery: the ship's commander, Captain Magane Hyuga, is his father—previously believed dead in a maritime accident near Antarctica during Goh's childhood. This revelation strains their relationship as Goh confronts his father about abandoning their family to command the Ra.

Goh develops a close bond with Annette, an emissary sent by the subterranean civilization to monitor humanity. When Annette defects to humanity's side, Goh becomes fiercely protective of her, especially after her childhood friend Avatar awakens and launches a devastating assault on the surface. Goh's hot-blooded, impulsive nature drives his actions: he instigates a helicopter brawl, nearly assaults his father during their tense reunion, and impulsively steals a dieselpunk seaplane from the Ra to rescue Annette mid-battle.

Across the narrative, Goh evolves from a disillusioned individual grappling with parental abandonment into an active participant in humanity's defense. His father symbolically passes the family sword to him, representing acknowledgment and the weight of legacy. Goh later uses this sword to free himself during a critical moment aboard the enemy vessel Liberty. By the conclusion, he reconciles with his father and joins the Ra's ongoing mission to confront the subterranean threat at its source.