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Over 2,000 years ago, the Mu Kingdom sank beneath the Pacific Ocean when a huge earthquake swept across its continent. Its submerged civilization survived, however, and harnessed the energy from the center of the earth. With this power, the Mu queen plans to conquer and subjugate the world. As disasters, including an earthquake in Tokyo, erupt all over the globe, the United Nations send their newest atomic submarine to search for the Mu Kingdom; but the craft is destroyed by underwater pressure emanating from the undersea empire. The only hope of salvation for the world is the Atragon , an extraordinary land-air-sea warship designed by a former Japanese naval commander who disappeared to a remote island when World War II ended in defeat for Japan. Although attempts by the Mu people to kidnap the commander, Captain Shinguji, have failed, they have succeeded in abducting both his daughter and her photographer boyfriend. The young people escape, taking the Mu queen captive, and Captain Shinguji consents to send the Atragon to defend Japan and the world. The vessel destroys all of the enemy's protective forces, including a monstrous sea creature, and then, by disabling the Mus' power source, destroys the entire Mu Kingdom.