Set up as a follow-up episode, Hokum Hare and the Turtles hitch a ride on a time-traveling train to 2036, where they discover that Shredder has plans for the future New York City. Ultimately, the Turtles of both the past and the future must team up to thwart Shredder before his actions cause all of time to be destroyed.

A delivery boy accidentally falls into Krang's new unstable Mutagen and becomes able to transform into anyone he chooses. Shredder tricks him into helping him launch the Mutagen into space and mutate the world, but this "Mutagen Man" has other ideas.