Episode 1: A Deep Sea Explorer Disappeared!
In year 20xx, there has been a series of mysterious accidents around the Japan Trench. The Japanese government secretly requests that Oki ' s Ocean Lab ' s Dr. Oki and Goro investigate the Ocean Empire, which is the prime suspect for the accidents, then they go missing. Before Dr. Oki and Goro leave the port on a bathyscaph, they hand Goro ' s younger brother, Susumu, the key to the lab ' s underground factory with a 99 logo and a rifle, model 99.
Episode 2: Scramble, the Super Submarine!
On Kairyumaru ' s deck, Susumu holds his tears, staring at the sea where his grandfather and brother were lost. Namino cheers him up and motivates him to find out the truth. However, the Ocean Empire ' s spies capture him and he gives up the key to the underground factory. Inside the dock of the underground factory lies Submarine Super 99.
Episode 3: Battle at 39600 Feet Deep!
Submarine Super 99 leaves Oki ' s Ocean Lab. Then, Americe ' s K-6 gets attacked by an unidentified submarine and sends an SOS to 99. 99 rushes to the site where the enemy ' s nuclear sub awaits!
Episode 4: The Ambush Achieved Great Success!
X-0 disappears in front of Submarine Super 99. X-0 ' s commander orders Stronestro to destroy 99, however, Stron and Stroger lose faith in the Ocean Empire ' s mission and fake an explosion of 99.
Episode 5: Challenge of A Young Warrior
Super 99 enters a dangerous zone in the Japan Trench where the Ocean Empire could be located. All crew get ready for battle. The Ocean Empire on the other hand is building a super submarine, type Z.
Episode 6: Hold-Up
Susumu passes out on a capsule in the fast underwater current. He wakes up as a hostage to the Ocean Empire. Susumu meets Stron and Stroger again. They tell him that they are Water World Men who live under water.
Episode 7: A Booby Trap!
Dr. Oki and Goro are still taken hostage by the Ocean Empire. Supreme Commander, Hell Deathbird, requests for secret documents on J engine, which is necessary for setting up a fleet of super submarines, in exchange for their lives. Susumu gives the enemy the documents.
Episode 8: Coronation of Emperor Is Declared!
At the Ocean Empire, Super Submarine, type Z, is under construction. Hell Deathbird takes his first step to achieve his desire and tells Queen Ze Violencia that he will take the throne as an emperor instead of her. On the other hand, Susumu tells Stronestro that humans and Water World Men should come together to live in peace.
Episode 9: Decision of A Great General
Submarine Super 99 heads for the Ocean Empire. Captain Oyama uses Dr. Oki ' s visual sonar to prepare for battle. Hell sends out a new fleet to attack 99 and tells General Zelbert to get rid of Dr. Oki and Goro. However, Zelbert realizes that he no longer wishes to help Hell.
Episode 10: Blast the Ocean Empire!
Goro and Dr. Oki come out of the enemy sub with a white flag to reunite with Susumu after a long time. After Zelbert betrays Hell, Hell tries to blow up the Ocean Empire, sacrificing everyone, and leave for a new place with Strait. Water World Men are still underneath the Ocean Empire.
Episode 11: Farewell, the Great General!
The Ocean Empire starts falling. Hell was betrayed by Zelbert and tried to blow up the whole empire. Zelbert survives but feels sorry for the many lives sacrificed and asks Oyama to let him have Hell.
Episode 12: Decisive Battle
Hell Deathbird heads for Underwater Sea. Strait has an internal conflict over Hell who destroyed her tribe. Stroger reunites with Susumu and guides 99 to find Hell. Where Yanna waits to destroy intruders, Oyama uses a repair sub as a dummy to send out 99 ' s sound waves, then 99 penetrates into Underwater Sea.
Episode 13: Embark to A New Ocean!
Submarine Super 99 goes into the underground sea. Crew investigates a hollow to find a giant tree which the legend says Water World Men were born from. They meet Queen Ze Violencia and suggest that all Water World Men leave the underground sea which is being contaminated by radiation. Crew accommodate Water World Men inside 99 ' s tank to escape. However, Hell Deathbird is determined to fight his final battle with 99.