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.