Against a world bracing for a Mu-driven crisis, Captain Jinguji Jun Tazaki stands at the helm of a daring project: a colossal, heavily armed submarine named Gotengo, a creation some call humanity’s last line of defense and potentially a path to reviving Japan’s war-time status after its defeat. As nations rally their forces, the mysterious reappearance of the Mu Empire casts a long shadow, threatening peace and forcing unlikely allies to reconsider how to respond. The stage is set for a high-stakes confrontation that could redefine who survives the era of secrecy and siege.
On a night of magazine photography, Susumu and Yoshito Nishibe Yū Fujiki are pulled into a strange sequence when a car drives straight into the ocean. The next day, after speaking with a detective, they spot Makoto Jinguji Yōko Fujiyama and learn she is being shadowed by a suspicious pursuer. The threads tighten as her father’s former superior, Rear Admiral Kusumi Ken Uehara, confronts a peculiar reporter who claims that Captain Jinguji is alive and hard at work on a new submarine project. The situation grows even more tangled when the reporter’s claims hint at a hidden base and a weapon that could alter the balance of power.
A mysterious package inscribed with the letters MU arrives for Kusumi. Inside lies a film showing Mu’s thriving undersea metropolis, complete with its own geothermal “sun,” and a chilling demand that the surface world capitulate and stop Jinguji from completing the Atragon, the submarine named Gotengo. The UN quickly recognizes the potential global danger and urges Kusumi to appeal directly to Jinguji, hoping to avert a catastrophe that could engulf much of the world. Concurrently, Makoto’s stalker is arrested and revealed to be a naval officer under Jinguji, who agrees to guide the party to Jinguji’s base but refuses to divulge its precise location.
After days of travel, the group arrives at a tropical island that hides Jinguji’s formidable forces and a vast underground dock. There, Captain Jinguji greets the visitors but treats his daughter with cool reserve, and his stance irks Kusumi, who pleads for a cause greater than personal loyalties. Makoto runs off in anger, only to be consoled later by Susumu, while the Gotengo undergoes a test run that proves its prowess—rapidly rising from the sea and dancing out of the water like a crowded, armored leviathan.
The fragile peace fractures when Susumu and the others are captured again, and Makoto is taken as well, as the base is crippled by a bomb planted by the Mu infiltrator. In the face of this aggression, Jinguji agrees to Kusumi’s request and readies Gotengo for war against Mu. Mu launches a devastating assault on Tokyo, threatening to sacrifice prisoners to the monstrous deity Manda if the Atragon dares to surface. The mighty Gotengo answers the call, pursuing a Mu submarine to Mu’s underwater empire and its enigmatic gateway to the oceans’ depths.
In a dramatic turn, Susumu and the other prisoners escape and kidnap Mu’s Empress [Tetsuko Kobayashi], defying the deity’s fiercest guardian, Manda. They are briefly thwarted by Manda itself, but Gotengo reenters the fray to rescue them and engages the creature with relentless resolve, ultimately freezing Manda with the absolute zero cannon. With the threat momentarily quelled, Jinguji offers to hear peace terms, but the Empress refuses to yield to negotiation. Undeterred, Jinguji drives Gotengo into Mu’s power room, freezing its geothermal machinery and collapsing Mu’s fortress of power before finally surfacing again.
The cataclysm that follows is spectacular, visible even to those standing on the deck of the surfaced Gotengo. As Mu’s empire dissolves in the fire and smoke, the Empress abandons the Atragon and, amid the conflagration, swims into the inferno alongside the fading world she sought to command. The tale closes with the fragile hope that humanity’s surfacing guardians can endure the cost of defending a fragile peace, even as the shadows of Mu linger in memory.
