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Some TMNT stuff really isn't for little kids.
Because Archie Comics' Teenage Mutant Ninja Turtles Adventures initially branched off from the continuity of the 1987 TV series, the Technodrome is located first under New York City, then in Dimension X. Later in the comics, Krang re-builds it into a spacecraft called the Skullbuzzer. Once Krang had been defeated, Cherubae gave the spacecraft to Stump's team after which it was not seen again.