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 the mutanimals. But the worms' effect was easily reverted by using sound waves to make their victims puke.
- 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 Karai needs to take daily doses of mind control serum so she won't fall back to Splinter's side.
- The Fourfold Trap - Karai trapped the turtles under to lure Splinter to fight her, after using the healing hands technique Karai fleed to a unknown part of the sewers where she spitted the worm out.