| Title | Season | Episode # | First Aired |
|---|---|---|---|
| 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 |
| Secret Origins (1) | 2 | 32 | Saturday January 17, 2004 |
| Secret Origins (2) | 2 | 33 | Saturday January 24, 2004 |
| Secret Origins (3) | 2 | 34 | Saturday January 31, 2004 |
| The Ultimate Ninja | 2 | 35 | Saturday February 7, 2004 |
| Reflections | 2 | 36 | Saturday February 14, 2004 |
| Modern Love - The Return of Nano | 2 | 37 | Saturday February 21, 2004 |
| What a Croc | 2 | 38 | Saturday February 28, 2004 |
| Return to the Underground | 2 | 39 | Saturday March 6, 2004 |
| City at War (1) | 2 | 40 | Saturday March 13, 2004 |
| City at War (2) | 2 | 41 | Saturday March 20, 2004 |
| City at War (3) | 2 | 42 | Saturday March 27, 2004 |
| Junklantis | 2 | 43 | Saturday April 3, 2004 |
| The Golden Puck | 2 | 44 | Saturday April 10, 2004 |
| Rogue in the House (1) | 2 | 45 | Saturday April 17, 2004 |
| Rogue in the House (2) | 2 | 46 | Saturday April 24, 2004 |
| April's Artifact | 2 | 47 | Saturday May 1, 2004 |
| Return of the Justice Force | 2 | 48 | Saturday May 8, 2004 |
| The Big Brawl (1) | 2 | 49 | Saturday May 15, 2004 |
| The Big Brawl (2) | 2 | 50 | Saturday September 18, 2004 |
| The Big Brawl (3) | 2 | 51 | Saturday September 25, 2004 |
| The Big Brawl (4) | 2 | 52 | Saturday October 2, 2004 |