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| Season 1 |
| Ep 1: Things Change Ep 2: A Better Mousetrap Ep 3: Attack of the Mousers Ep 4: Meet Casey Jones Ep 5. Nano Ep 6. Darkness on the Edge of Town Ep 7: The Way of Invisbility Ep 8: Fallen Angel Ep 9: Garbageman Ep 10: The Shredder Strikes, Part One Ep 11: The Shredder Strikes, Part Two Ep 12: The Unconvincing Turtle Titan Ep 13: Notes from the Underground, Part One Ep 14: Notes from the Underground, Part Two Ep 15: Notes from the Underground. Part Three Ep 16: The King Ep 17: The Shredder Strikes Back, Part One Ep 18: The Shredder Strikes Back, Part Two Ep 19: Tales of Leo Ep 20: Monster Hunter Ep 21: Return to New York, Part One Ep 22: Return to New York, Part Two Ep 23: Return to New York, Part Three Ep 24: Lone Raph and Cub Ep 25: Search For Splinter, Part One Ep 26: Search For Splinter, Part Two |
| Season 2 |
| Ep 27: The Fugitoid Ep 28: The Trouble with Triceratons Ep 29: The Big House Ep 30: The Arena Ep 31: Triceaton Wars Ep 32: Secret Origins Part 1 Ep 33: Secret Origins Part 2 Ep 34: Secret Origins Part 3 Ep 35: The Ultimate Ninja Ep 36: Reflections Ep 37: Modern Love - The Return of Nano Ep 38: What a Croc! Ep 39: Return to the Underground Ep 40: City at War Part 1 Ep 41: City at War Part 2 Ep 42: City at War Part 3 Ep 43: Junklantis Ep 44: The Golden Puck Ep 45: Rogue in the House Part 1 Ep 46: Rogue in the House Part 2 Ep 47: April's Artifact Ep 48: Return of the Justie Force Ep 49: Big Brawl Part 1 Ep 50: Big Brawl Part 2 Ep 51: Big Brawl Part 3 Ep 52: Big Brawl Part 4 |
| Season 3 |
| Ep 53: The Christmas Aliens Ep 54: Space Invaders Part One Ep 55: Space Invaders Part Two Ep 56: Space Invaders Part Three Ep 57: Worlds Collide Part One Ep 58: Worlds Collide Part Two Ep 59: Worlds Collide Part Three Ep 60: Touch and Go Ep 61: Hunted Ep 62: H.A.T.E Ep 63: Nobody's Fool Ep 64: New Blood Ep 65: The Lesson Ep 66: The Darkness Within Ep 67: Mission of Gravity Ep 68: The Entity Below Ep 69: Time Travails Ep 70: Hun on the Run Ep 71: Reality Check Ep 72: Accross the Universe Ep 73: Same As It Never Was Ep 74: The Real World Part One Ep 75: The Real World Part Two Ep 76: Bishop's Gambit Ep 77: Exodus Part One Ep 78: Exodus Part Two |
| Episode Guide |
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| Season 4 |
| Ep 79: Cousin Sid Ep 80: The People's Choice Ep 81: Sons of the Silent Age Ep 82: Dragon's Brew Ep 83: I, Monster Ep 84: Grudge Match Ep 85: Wing and a Prayer Ep 86: Bad Day Ep 87: Aliens Among Us Ep 88: Dragons Rising Ep 89: Still Nobody Ep 90: All Hallows Thieves Ep 91: Samurai Tourist Ep 92: The Ancient One Ep 93: Scion of the Shredder Ep 94: Prodigal Son Ep 95: Outbreak Ep 96: The Trouble With Augie Ep 97: Insane In The Membrane Ep 98: Return of Savanti, Part 1 Ep 99: Return of Savanti, Part 2 Ep 100: A Tale of Master Yoshi Ep 101: Adventures In Turtle-Sitting Ep 102: Good Genes Part 1 Ep 103: Good Genes Part 2 Ep 104: The Nijna Tribunal |
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| Season 5 "Ninja Tribunal" |
| Ep 105: Lap of the Gods Ep 106: Demons and Dragons Ep 107: Legend of the Five Dragons Ep 108: More Worlds Than One Ep 109: Beginning of the End Ep 110: Nightmares Recycled Ep 111: Membership Drive EP 112: New World Order Part 1 Ep 113: New World Order Part 2 Ep 114: Fathers & Sons Ep 115: Past Present Ep 116: Enter the Dragons Part 1 Ep 117: Enter the Dragons Part 2 |
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