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The Mutagen Missile is a mutagen-weapon used by The Kraang in part 1 of Battle for New York, it was stationed in Kraang-occupied New York City when both the turtles and the Mighty Mutanimals heard about it, it is described by Jack Kurtzman as containing enough Mutagen to create another Dimension X.Both the Mighty Mutanimals and the Turtles come up with plans to destroy the missile, although Slash decides to do things his way. Despite their best efforts to prevent the launch, Kraang Subprime manages to launch the missile into the atmosphere, Donatello, who is still on the missile, manages to reconfigure the projected location and send the missile into the heart of the sun.

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