One of Professor Utonium's failed experiments causes everyone in the city to switch bodies. He must find a solution whilst the girls (in different bodies) fight Mojo Jojo, in the body of an old woman.
Criss Cross Crisis provides examples of:
- Animal Super Hero: the professors first attempt to restore everyone back to normal puts the girls in the bodies of a Cobra, a dog and a caterpillar.
- Ash Face: Mojo (in his old woman body) when the girls fry him with their eye beams.
- Evil Old Folks: Mojo becomes this because he switches bodies with an old woman.
- "Freaky Friday" Flip: Up to Eleven, since everyone in Townsville (and possibly the world) switches bodies due to the Professor's machine. The trope name even gets lampshaded in the form of an advertisement for a film called Freakin Friday.
- Irony: the second attempt to restore everyone ends with Mojo trapped in the body of a fish, and the girls in the bodies of a cook, a fisherman and an Inuit respectively.
- Lawyer-Friendly Cameo: Popeye shows up briefly in the fight near the end, albeit unnamed.
- Major Injury Underreaction: Mojo's reaction after the girls fry him with their eye beams is to say, "Ow. Oh. Ow. Ow. Ow. Ow. Ow. Ow. Ow. Ooh, ow."
- My God, What Have I Done?: Said word for word by the Professor after he accidentally causes the massive body swap.
- New Body, Old Abilities: no matter whose body they are in, the girls keep all of their superpowers. Likewise, Mojo, in the body of the old woman, still has his usual strength and agility while the old woman in Mojos body is still as frail as you expect an old lady like her to be. Handwaved by the Professor, who claims that his machine only switches the outer layers of things but not the inner, demonstrating as such with an apple that has the inside of an orange and an orange with the inside of an apple.
- Plot Hole: It's explicitly shown the body-switching doesn't change anyone's location, because it's actually the bodies that are changed, not the minds. Inexplicably, the people who switched bodies with Mojo Jojo, Fuzzy Lumpkins, and the Gangrene Gang are all located in said villains' usual residences, even treating them as if they were their own homes.
- Voices Are Mental: No matter whose body they are in, all characters retain their original voices.