| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Cousin Sid | 4 | 79 | Saturday September 10, 2005 |
| The People's Choice | 4 | 80 | Saturday September 17, 2005 |
| A Wing And A Prayer | 4 | 81 | Saturday September 24, 2005 |
| Sons Of The Silent Age | 4 | 82 | Saturday October 1, 2005 |
| Dragons' Brew | 4 | 83 | Saturday October 8, 2005 |
| I, Monster | 4 | 84 | Saturday October 15, 2005 |
| Grudge Match | 4 | 85 | Saturday October 22, 2005 |
| All Hallows Thieves | 4 | 86 | Saturday October 29, 2005 |
| Bad Day | 4 | 87 | Saturday November 5, 2005 |
| Aliens Among Us | 4 | 88 | Saturday November 12, 2005 |
| Dragon's Rising | 4 | 89 | Saturday November 19, 2005 |
| Still Nobody | 4 | 90 | Saturday November 26, 2005 |
| Samurai Tourist | 4 | 91 | Saturday December 3, 2005 |
| The Ancient One | 4 | 92 | Saturday December 10, 2005 |
| Scion of the Shredder | 4 | 93 | Saturday February 4, 2006 |
| Prodigal Son | 4 | 94 | Saturday February 11, 2006 |
| Outbreak | 4 | 95 | Saturday February 18, 2006 |
| The Trouble With Augie | 4 | 96 | Saturday February 25, 2006 |
| Insane in the Membrane | 4 | 97 | |
| A Tale of Master Yoshi | 4 | 98 | Saturday March 4, 2006 |
| Return of Savanti (1) | 4 | 99 | Saturday March 11, 2006 |
| Return of Savanti (2) | 4 | 100 | Saturday March 18, 2006 |
| Adventures in Turtle-Sitting | 4 | 101 | Saturday March 25, 2006 |
| Good Genes (1) | 4 | 102 | Saturday April 1, 2006 |
| Good Genes (2) | 4 | 103 | Saturday April 8, 2006 |
| The Ninja Tribunal | 4 | 104 | Saturday April 15, 2006 |