Brain Worms were created by Baxter Stockman so Shredder could get his "daughter" back via mind control.
- "Clash of the Mutanimals" - Baxter Stockman uses mutagen and the mind control serum to create the worms, which were injected in Raphael and two of the Mutanimals, Slash and Dr Rockwell. But the worms' effect was easily reverted by using things like sound waves to make their victims puke out the worm.
- "The Deadly Venom" - The worms are used to control Karai, who's ordered to destroy the Turtles and their allies.
- "Attack of the Mega Shredder!" - It's shown that Karai needs to take constant doses of the mind control serum so she won't fall back to Splinter's side.
- "The Fourfold Trap" - Karai trapped the Turtles and lured Splinter to fight her. After he used the Healing Hands technique on her, Karai fled to a unknown part of the sewers where she spat the worm out.