Submarine Super 99 (Japanese: 潜水艦スーパー99, Hepburn: Sensuikan Sūpā Nain Nain) is a manga series written and illustrated by Leiji Matsumoto.

The empire's military commander in chief, Hell Deathbird, demands that all shipping request his permission for sailing.

The story begins as Japanese forces decided to investigate the mysterious threat beneath the ocean.

Goro Oki gives his younger brother, Susumu, a rifle, a weapon modified from Type 99 rifle of the World War II era; Susumu is also given a key bearing a "99" marck by his grandfather Juzou.

Goro and Juzou Oki set off in an exploration submarine to investigate the attacks in the Japanese Trench; soon later, their vessel is attacked by a mysterious submarine hiding in the Trench.