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The legendary empire of the lost continent of Mu reappears to threaten the world with domination. While countries unite to resist, an isolated World War II Captain has created the greatest warship ever seen, and possibly the surface world's only defense.
While on a magazine photo shoot one night, photographers Susumu (Takashima) and Yoshito (Yu Fujiki) witness a car drive into the ocean. While speaking with a detective (Hiroshi Koizumi) the next day they spot Makoto Jinguji (Fujiyama), daughter of deceased Imperial Captain Jinguji, who is also being followed by a suspicious character (Yoshifumi Tajima). Her father's former superior, retired Rear Admiral Kusumi (Ken Uehara), is confronted by a peculiar reporter (Kenji Sahara) who claims contrarily that Captain Jinguji is alive and at work on a new submarine project. The threads meet when a mysterious taxi driver (Akihiko Hirata) almost abducts Makoto and the Admiral, claiming to be an agent of the drowned Mu Empire. Foiled by the ensuing photographers, he flees into the ocean.
During another visit to the detective, a packaged inscribed "MU" arrives for the Admiral. Contained within is a film depicting the thriving undersea continent (with its own geothermal "sun") and demanding that the surface world capitulate, and prevent Jinguji from completing his submarine Atragon. The UN realizes that Atragon may be the world's only defense and requests that Admiral Kosumi appeal to Jinguji. Concurrently, Makoto's stalker is arrested and discovered to be a naval officer under Jinguji. He agrees to lead the party to Jinguji's base but refuses to disclose its location. After several days of travel, the party find themselves on a tropical island inhabited only by Jinguji's forces and enclosing a vast underground dock.
Eventually Captain Jinguji (Tazaki) greets the visitors, though he is cold toward his daughter and infuriated by Kusumi's appeal. He built Atragon, he explains, as a means to restore the Japanese Empire after its defeat in World War II, and insists that it be used for no other purpose. Makoto runs off in anger, later to be consoled by Susumu. Atragon's test run is a success, the heavily-armored submarine even elevating out of the water and flying about the island. When the Captain approaches Makoto that evening they exchange harsh words; again Susumu reproaches the Captain for his selfish refusal to come to the world's aid. After daughter and boyfriend are abducted by the reporter (a disguised Mu agent) and the base crippled by a bomb, Jinguji consents to Kusumi's request and prepares Atragon for war against Mu.
The Mu Empire executes a devastating attack on Tokyo and threatenes to sacrifice its prisoners to the monstrous deity Manda if Atragon appears. Appear the super-submarine does, pursuing a Mu submarine to the Empire's entrance in the ocean depths. Meanwhile, Susumu and the other prisoners escape their cell and kidnap the Empress of Mu (Tetsuko Kobayashi). They are impeded by Manda, but soon rescued by Atragon, which then engages the serpent and freezes it using the "Absolute Zero Cannon". Jinguji offers to hear peace terms, but the proud Empress refuses. The Captain then advances Atragon into the heart of the Empire and freezes its geothermal machinery. This results in a cataclysmic explosion visible even to those on deck of the surfaced submarine. Her empire dying, the Mu Empress abandons the Atragon and, Jinguji and company looking on, swims into the conflagration.
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