Shiro Kaieda is appointed the captain of Japan's first nuclear submarine, jointly built by Japan and the United States in top secret. However, he and his 76 crew members go rogue in this story that delves into themes of nuclear war, international politics, and world peace.

In the freezing northern seas, the Yamato nuclear submarine begins its deep underwater voyage to the tune of Mozart, heading for the United Nations headquarters in New York. In the Bering Strait between the US and Russia, another submarine approaches: an American nuclear submarine that overwhelmingly dwarfs the Yamato. Now, a battle commences among the cracking floes of the cold Arctic Ocean.