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They appear as guest stars in The Adventures of Super Mario Bros. 3 episode "Kootie Pie Rocks", voiced by their real selves. In the episode, the Mario Brothers go to Brooklyn with Princess Toadstool for a Milli Vanilli concert. However, Cheatsy Koopa overhears them talking about this and tells Kootie Pie back at Castle Koopa, who is enraged that she can't go. In the middle of the band's concert, however, the Doomship arrives and King Koopa kidnaps them. They are taken back to Castle Koopa, where Kootie Pie wants them to sing for her. The two refuse, which leads to Kootie Pie using her Magic Wand to turn them into accountants, and she tells them that they will be trapped in Dark Land forever unless they perform for her. When they try to escape, but two Sledge Brothers block the exit. Kootie Pie then threatens to transform them again, but Milli Vanilli tell her that they can't perform without a backup band.
Mario, Luigi, the Princess, and Toad take advantage of this and disguise themselves as a band to sneak inside Castle Koopa (Milli Vanilli recognizing Toadstool from the audience at the concert) and trick Kootie Pie into turning the band back to normal. When Milli Vanilli tries to perform with them, however, Mario and friends play cannot play their instruments, and everyone in the castle flees from the terrible music, allowing them to escape. Back at their proper concert in Brooklyn, Milli Vanilli dedicate their next song to Princess Toadstool.
Milli Vanilli was the only celebrity appearance on The Adventures of Super Mario Bros. 3, with Rob Pilatus and Fab Morvan providing their voices for their animated counterparts.
Milli Vanilli was accused of lip-synching, which in November 1990 they finally confessed to. Glitches in their equipment revealed this only two weeks after the initial airing of "Kootie Pie Rocks", and one week after the group won the 1990 Grammy Awards, which they relinquished. Subsequent airings of the cartoon cut their songs and replaced them with different instrumental music (the pair still move their lips while performing these songs in the re-releases, however, as the episodes were not reanimated to reflect the change), as well as cutting any references to Milli Vanilli throughout the episode. Milli Vanilli's song at the episode's end was completely cut, without even an instrumental replacement.