| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Tempus Fugit | 7 | 143 | |
| The Ancient One | 4 | 92 | Saturday December 10, 2005 |
| 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 |
| The Christmas Aliens | 3 | 64 | Saturday December 25, 2004 |
| The Cosmic Completist | 6 | 140 | Saturday October 13, 2007 |
| The Darkness Within | 3 | 66 | Saturday January 29, 2005 |
| The Day of Awakening | 6 | 141 | Saturday October 20, 2007 |
| The Entity Below | 3 | 68 | Sunday February 6, 2005 |
| The Freaks Come Out at Night... | 6 | 127 | Saturday November 25, 2006 |
| The Gaminator | 6 | 130 | Saturday December 16, 2006 |
| The Golden Puck | 2 | 44 | Saturday April 10, 2004 |
| The Journal | 6 | 129 | Saturday December 9, 2006 |
| The King | 1 | 16 | Saturday May 31, 2003 |
| The Lesson | 3 | 63 | Saturday December 18, 2004 |
| The Monster Hunter | 1 | 20 | Saturday September 20, 2003 |
| The Ninja Tribunal | 4 | 104 | Saturday April 15, 2006 |
| The People's Choice | 4 | 80 | Saturday September 17, 2005 |
| The Real World (1) (4) | 3 | 74 | Saturday March 26, 2005 |
| The Real World (2) (5) | 3 | 75 | Saturday April 2, 2005 |
| The Search for Splinter (1) | 1 | 25 | Saturday October 25, 2003 |
| The Search for Splinter (2) | 1 | 26 | Saturday November 1, 2003 |
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