Interrupting an early experiment by the Kraang involving their latest invention which allows the alien beings to transfer their minds into human leaders around the world paving the way for the Kraang’s takeover of the planet, Raphael‘s (Sean Astin) mind is accidentally switched with that of a Kraang.
Mistakenly taking Raphael’s Kraang-controlled body with them after the attack, Leonardo (Jason Biggs), Michelangelo (Greg Cipes), and Donatello (Rob Paulsen), with the help of Casey Jones (Josh Peck) and April (Mae Whitman), use the Turtle Sub to break into the Technodrome and find Raphael whose odd behavior is beginning to make the other Kraang suspicious. But before they can save their brother they’ll have to deal with a sea creature who takes a bit too much liking to the Turtle Sub for comfort.
The Freaky Friday set-up creates some enjoyable moments of Raphael attempting to pass himself off as Kraang as well as the Kraang Turtle’s attempts ask directions back to the Technodrome from various New Yorkers. Eventually the Turtles manage to get Raphael back in the right body (and Casey and April switched back as well after temporarily jumping bodies during the attack), destroy the machine, and delay the Kraang’s plans for world domination for another day.