| Title | Season | Episode # | First Aired |
|---|---|---|---|
| A Better Mousetrap (1) | 1 | 2 | Saturday February 15, 2003 |
| A Tale of Master Yoshi | 4 | 98 | Saturday March 4, 2006 |
| A Wing And A Prayer | 4 | 81 | Saturday September 24, 2005 |
| Across The Universe (2) | 3 | 72 | Saturday March 12, 2005 |
| Adventures in Turtle-Sitting | 4 | 101 | Saturday March 25, 2006 |
| Aliens Among Us | 4 | 88 | Saturday November 12, 2005 |
| All Hallows Thieves | 4 | 86 | Saturday October 29, 2005 |
| April's Artifact | 2 | 47 | Saturday May 1, 2004 |
| Attack of the Mousers (2) | 1 | 3 | Saturday February 22, 2003 |
| Bad Blood | 6 | 128 | Saturday December 2, 2006 |
| Bad Day | 4 | 87 | Saturday November 5, 2005 |
| Beginning of the End | 5 | 109 | Saturday March 15, 2008 |
| Bishop to Knight | 6 | 122 | Saturday October 14, 2006 |
| Bishop's Gambit | 3 | 76 | Saturday April 9, 2005 |
| 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 |
| Clash of the Turtle Titans | 6 | 124 | Saturday October 28, 2006 |
| Cousin Sid | 4 | 79 | Saturday September 10, 2005 |
| Darkness on the Edge of Town | 1 | 6 | Saturday March 15, 2003 |
| Demons and Dragons | 5 | 106 | Saturday February 23, 2008 |
| DNA is Thicker Than Water | 6 | 139 | Saturday October 6, 2007 |
| Dragon's Rising | 4 | 89 | Saturday November 19, 2005 |
| Dragons' Brew | 4 | 83 | Saturday October 8, 2005 |
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