Raphael accidentally damages a machine that forces him to swap minds with a Kraang. Now he must find a way to convince his brothers and Splinter that it's really him, before the Kraang controlling his body destroys his brothers or worse, reveals their location to the rest of the Kraang.

The Shredder kidnaps and experiments on the Mighty Mutanimals.

Usagi and the turtles must help Kintaro fulfill his destiny as they reach the end of their journey.