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:
- Ad-Break Double-Take: Before and after the commercial break, Mojo Jojo (in the old lady's body) says, "A priceless vase, and I have taken it for myself without paying!"
- 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.
- Cultural Cross-Reference: Totoro is among the body-swapped people seen at the bank.
- 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."
- Mirror Reveal: Blossom finds out that she's in Miss Bellum's body when Buttercup (in the Professor's body) holds a mirror up to her. Afterward, Bubbles, in the Mayor's body, walks over to the bathroom mirror and has this hilarious Double Take.Bubbles: Mayor, what are you doing in our house. I'm not in your house, you're in my body. Oh. (beat; cue Spit Take)
- 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 the process is actually changing bodies, not moving around 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.
- Post Wake Up Realization: Happens three times in succession, in which the girls realize that they've gained new bodies thanks to the Professor's latest invention gone wrong.
Bubbles: Mayor, what are you doing over at our house? Oh, I'm not in your house, you're in my body. (continues brushing until her eyes pop open and does a Spit Take)
- As the Professor goes to wake up Buttercup, she gets up to tell him to quit bothering her. She goes back under her covers, then goes into a Double Take to see that the Professor has her body and that she has his.
- As Buttercup has a meltdown, Blossom rises to tell her to shut up, unaware that she now has Miss Bellum's body. She finds this out when Buttercup produces a hand mirror for her to look into.
- Finally, Bubbles finds out she's in The Mayor's body when she gets out of bed, half-asleep, and sees her reflection in the bathroom mirror while brushing her teeth. And even then, she doesn't realize it at first and believes she's seeing the real Mayor.
- Troll: When the Professor's invention finally puts everyone back in their own bodies (after rapid-fire cycling through several more swaps and going "Nope!" with each one), he pauses and cheerfully says "Nope!", then grins devilishly to himself after the Mayor and Ms. Bellum stop him from re-scrambling everyone again.
- Voices Are Mental: No matter whose body they are in, all characters retain their original voices.