Season 1
- "Mystic Mayhem" (debut)
- "Origami Tsunami"
- "Donnie's Gifts"
- "War and Pizza"
- "Newsworthy"
- "Down with the Sickness"
- "Mascot Melee"
- "The Fast and the Furriest"
- "Shell in a Cell"
- "Minotaur Maze"
- "Bug Busters"
- "The Longest Fight"
- "Hypno! Part Deux"
- "The Gumbus"
- "Mrs. Cuddles"
- "Stuck on You"
- "Al Be Back"
- "The Purple Jacket" (minor)
- "Pizza Pit"
- "The Evil League of Mutants"
- "Smart Lair"
- "Hot Soup: The Game" (minor)
- "Late Fee"
- "Bullhop"
- "Mind Meld"
- "Portal Jacked!"
- "Shadow of Evil"
- "Operation: Normal"
- "Sparring Partner"
- "Warren and Hypno, Sitting in a Tree"
- "You Got Served"
- "How to Make Enemies and Bend People to Your Will"
- "Mystic Library"
- "The Purple Game"
- "Man VS. Sewer"
- "The Mutant Menace"
- "Turtle-dega Nights: The Ballad of Rat Man" (minor)
- "The Ancient Art of Ninja Hide and Seek"
- "One Man's Junk"
- "Snow Day"
- "Cloak and Swaggart" (minor)
- "Jupiter Jim Ahoy!"
- "Insane in the Mama Train"
- "End Game"
Season 2
- "Flushed but Never Forgotten"
- "Lair Games"
- "Many Unhappy Returns"
- "Todd Scouts"
- "Goyles, Goyles, Goyles" (flashback only) (mutates in flashback) (no lines)
- "Repairin' the Baron" (minor)
- "Air Turtle"
- "Pizza Puffs"
- "Sidekick Ahoy!"
- "Donnie vs. Witch Town" (minor)
- "Raph's Ride-Along" (minor)
- "Hidden City's Most Wanted" (minor)
- "Bad Hair Day"
- "Fists of Furry" (minor)
- "The Clothes Don't Make the Turtle"
- "Battle Nexus: New York"
- "E-Turtle Sunshine of the Spotless Mind"
- "Shreddy or Not"
- "Anatawa Hitorijanai"
- "Rise"
Shorts
- "Race"
- "Turtle Tots"