In the year 20XX AD, mysterious shipwrecks have been continuing to occur near Japan. Oki Juzo and Itsuro disappears to investigate these incidents. Just before they left, they came by a key engraved with the letters "SS-99" in the underground lab where Juzou's grandchild and Itsuro's younger brother, a senior high student Oki Shinji, had been improving various "99 Shikipo Heichu" rifles.

As the two progresses in their investigation, the two get caught when they sneak into a laboratory and are lead to a workshop underground. There, one never seen before huge submarine rests.

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Other: Uchuu Kaizoku Captain Herlock