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In the GBA TMNT game, the Time Scepter is a trophy you get for finishing all acts quickly.
The Time Scepter makes a re-appearance in the packed-in comic book for Teenage Mutant Ninja Turtles Smash-Up, where Donatello uses it in an attempt to instantaneously transport the Turtles, Splinter, April, and Casey to The Shredder's Japanese headquarters. The Scepter malfunctions, and the group ends up hopping to an Amazon rainforest and feudal Japan before finally arriving at their destination.