In the near future, the world is at war: the USR, a mysterious organization led by Admiral Red and his powerful submarine UX, wants to stop human exploitation of the seas, having torpedoed many ships and ports. The world's navies unite and form the Peace Keeping Navy, or PKN, to fight the "terrorists". Every major UN member contributed a submarine, though the Japanese entry is an old clunker, the 707, and it is running late to the inaugural meeting. When the meeting finally begins, Admiral Red and the UX come to spoil the show with a spread of torpedoes. Arriving late in the battle, Captain Youhei Hayami steers the 707 into the way of a torpedo launched at the supercarrier that serves as the PKN's flagship. His ship is destroyed, but the flagship survives.

Six months later, Captain Hayami is given command of the salvaged and rebuilt 707, and takes a crew of old comrades and brand new cadets to sea to fight Admiral Red once more.