| Title | Season | Episode # | First Aired |
|---|---|---|---|
| The Shredder Strikes (1) | 1 | 10 | Saturday April 12, 2003 |
| The Shredder Strikes (2) | 1 | 11 | Saturday April 19, 2003 |
| The Shredder Strikes Back (1) | 1 | 17 | Saturday June 7, 2003 |
| The Shredder Strikes Back (2) | 1 | 18 | Saturday June 14, 2003 |
| The Trouble With Augie | 4 | 96 | Saturday February 25, 2006 |
| The Ultimate Ninja | 2 | 35 | Saturday February 7, 2004 |
| The Unconvincing Turtle Titan | 1 | 12 | Saturday May 3, 2003 |
| The Way of Invisibility | 1 | 7 | Saturday March 22, 2003 |
| Things Change | 1 | 1 | Saturday February 8, 2003 |
| Time Travails | 3 | 69 | Monday February 7, 2005 |
| Timing Is Everything | 6 | 132 | Saturday March 31, 2007 |
| Touch and Go | 3 | 59 | Saturday November 20, 2004 |
| Turtle X-tinction | 6 | 136 | Saturday April 28, 2007 |
| Turtles in Space (1): The Fugitoid | 2 | 27 | Saturday November 8, 2003 |
| Turtles in Space (2): The Trouble with Triceratons | 2 | 28 | Saturday November 15, 2003 |
| Turtles in Space (3): The Big House | 2 | 29 | Saturday November 22, 2003 |
| Turtles in Space (4): The Arena | 2 | 30 | Saturday November 29, 2003 |
| Turtles in Space (5): Triceraton Wars | 2 | 31 | Saturday December 6, 2003 |
| What a Croc | 2 | 38 | Saturday February 28, 2004 |
| Worlds Collide (1) | 3 | 56 | Saturday October 30, 2004 |
| Worlds Collide (2) | 3 | 57 | Saturday November 6, 2004 |
| Worlds Collide (3) | 3 | 58 | Saturday November 13, 2004 |
| Zixxth Sense | 6 | 142 | Saturday October 27, 2007 |
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