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In The Super Mario Bros. Super Show! episode "20,000 Koopas Under the Sea", the Koopilus first appears in Happy Harbor to destroy and devour a ship, before unsuccessfully trying to attack Mario, Luigi, Toad and Princess Toadstool, who are on a nearby dock.
King Koopa causes more havoc around the town with the submarine. His plan is to promise to save the town from the Koopilus, which the inhabitants believe to be a sea monster, if they make him their ruler. This plan is ruined due to the intervention of Mario, Luigi, Toad, Princess Toadstool and Captain Abidab, who reveal King Koopa's malevolent attitude before they decide to hunt for the Koopilus themselves.
While venturing underwater, Mario, Luigi, Toad, Princess Toadstool and Captain Abidab are ambushed by the Koopilus, which Mario manages to hit on the head with a plunger launched from a harpoon gun. Mario, Luigi and Princess Toadstool are subsequently dragged through the water by it. It is only when the submarine dives under an arch-shaped rock that the rope attached to it snaps, dropping the group onto the ocean floor. As they try to run away, the Koopilus devoures them. Toad and Captain Abidab flee and hide from it. Following it to the surface, the two of them catch sight of it bashing into Captain Abidab's ship, the Peapod, before submerging once more.
On the inside of the Koopilus, Koopa Nemo appears before Mario, Luigi and Princess Toadstool and reveals that the monster is actually a submarine, also revealing his plans to use it to destroy Happy Harbor. Koopa Nemo proceeds to make the three of them his galley slaves and make them peel onions in the kitchen of the Koopilus.
The submarine starts its attack on Happy Harbor with the ships near it. Captain Abidab launches Toad into its mouth, having received a message in a bottle from Mario revealing the Koopilus' true nature. Once inside it, Toad locates and frees Mario, Luigi and Princess Toadstool, only to be chased outside by four of Koopa Nemo's Bloober minions.
The Koopilus eventually meets its end when Super Mario and Super Luigi, after defeating Koopa Nemo's Bloober henchmen, leap from the water and onto its head. After several attempts to shake Mario and Luigi off the Koopilus, Koopa Nemo succeeds in doing so, only to lose control of it and crash it into Happy Harbor, where it explodes.