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Season One
- "Rise of the Turtles, Part 1"
- "Rise of the Turtles, Part 2"
- "Turtle Temper"
- "New Friend, Old Enemy"
- "I Think His Name is Baxter Stockman"
- "Metalhead"
- "Monkey Brains"
- "Never Say Xever"
- "The Gauntlet"
- "Panic in the Sewers"
- "Mousers Attack!"
- "It Came From the Depths"
- "I, Monster"
- "New Girl in Town"
- "The Alien Agenda"
- "The Pulverizer"
- "TCRI"
- "Cockroach Terminator"
- "Baxter's Gambit"
- "Enemy of My Enemy"
- "Karai's Vendetta"
- "Pulverizer Returns"
- "Parasitica"
- "Operation: Break Out"
- "Booyaka-Showdown, Part 1"
- "Booyaka-Showdown, Part 2"
Season Two
- "The Mutation Situation"
- "Invasion of the Squirrelanoids"
- "Follow The Leader"
- "Mutagen Man Unleashed"
- "Mikey Gets Shellacne"
- "Target: April O'Neil"
- "Slash and Destroy"
- "The Good The Bad And Casey Jones"
- "The Kraang Conspiracy"
- "Fungus Humungous"
- "Metalhead Rewired"
- "Of Rats and Men"
- "The Manhattan Project, Part 1"
- "The Manhattan Project, Part 2"
- "Mazes And Mutants"
- "The Lonely Mutation of Baxter Stockman"
- "Newtralized"
- "Pizza Face"
- "The Wrath of Tiger Claw"
- "The Legend of the Kuro Kabuto"
- "Plan 10"
- "Vengeance is Mine"
- "A Chinatown Ghost Story"
- "Into Dimension X"
- "The Invasion, Part 1"
- "The Invasion, Part 2"
Season Three
- "Within The Woods"
- "A Foot Too Big"
- "Buried Secrets"
- "The Croaking"
- "Dream Beavers" note
- "Race With the Demon"
- "Eyes of the Chimera"
- "Vision Quest"
- "Return to New York"
- "Serpent Hunt"
- "The Pig And the Rhino"
- "Battle For New York, Part 1"
- "Battle For New York, Part 2"
- "Casey Jones VS. The Underworld"
- "The Noxious Avenger"
- "Clash Of The Mutanimals"
- "Meet Mondo Gecko"
- "The Deadly Venom"
- "Turtles In Time"
- "Tale Of The Yokai"
- "Attack Of The Mega Shredder!"
- "The Creeping Doom"
- "The Fourfold Trap"
- "Dinosaur Seen In Sewers!"
- "Annihilation Earth!, Part 1"
- "Annihilation Earth!, Part 2"
Season Four
- "Beyond The Known Universe"
- "The Moons of Thalos 3"
- "The Weird World Of Wyrm"
- "The Outlaw Armaggon!"
- "Riddle Of The Ancient Aeons"
- "Journey to the Center of Mikey's Mind"
- "The Arena of Carnage"
- "The War for Dimension X"
- "The Cosmic Ocean"
- "Trans-Dimensional Turtles"
- "Revenge of the Triceratons"
- "The Evil of Dregg"
- "The Ever-Burning Fire"
- "Earth's Last Stand"
- "City At War"
- "Broken Foot"
- "The Insectra Trifecta"
- "Mutant Gangland"
- "Bat in the Belfry"
- "The Super Shredder"
- "Darkest Plight"
- "The Power Inside Her" note
- "Tokka vs. The World"
- "Tale of Tiger Claw"
- "Requiem"
- "Owari"
Season Five (Tales of the Teenage Mutant Ninja Turtles)
- "Scroll of the Demodragon"
- "The Forgotten Swordsman"
- "Heart of Evil"
- "End Times"
- "When Worlds Collide" note
- "Yojimbo" note
- "Osoroshi No Tabi" note
- "Kagayeki! Kintaro" note
- "Lone Rat And Cubs"
- "Raphael: Mutant Apocalypse" note
- "The Curse of Savanti Romero"
- "The Crypt of Dracula"
- "The Frankenstein Experiment"
- "Monsters Among Us!"
- "Wanted: Bebop and Rocksteady"
- "The Foot Walks Again!"
- "The Big Blowout"