Submarine Super 99 contans episodes 1-13 of the anime directed by Hiromichi Matano.

In the 21st century, a series of unexplained shipwrecks are occurring near the Japan Trench. The government makes a top secret request to Juzou Oki, the director of the Oki Ocean Lab, and his son, Goro, the deputy director. The two of them begin to investigate the incidents in a bathyscaphe, but are attacked by a mysterious submarine and go missing. Susumu Oki, Juzou's other grandson and Goro's younger brother, had earlier been given a rifle, "SS-99," and the key to a basement factory. Soon, spies break into the lab and force Susumu to take them to the basement factory, where they see a gigantic submarine...

Special Features: Clean Opening, Clean Endings, Leiji Matsumoto interview