| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Future Shellshock! | 6 | 117 | Saturday July 29, 2006 |
| Obsolete | 6 | 118 | Saturday August 5, 2006 |
| Home Invasion | 6 | 119 | Saturday August 12, 2006 |
| Headlock Prime | 6 | 120 | Saturday September 30, 2006 |
| Playtime's Over | 6 | 121 | Saturday October 7, 2006 |
| Bishop to Knight | 6 | 122 | Saturday October 14, 2006 |
| Night of Sh'Okanabo! | 6 | 123 | Saturday October 21, 2006 |
| Clash of the Turtle Titans | 6 | 124 | Saturday October 28, 2006 |
| Fly Me to the Moon | 6 | 125 | Saturday November 4, 2006 |
| Invasion of the Bodyjacker | 6 | 126 | Saturday November 11, 2006 |
| The Freaks Come Out at Night... | 6 | 127 | Saturday November 25, 2006 |
| Bad Blood | 6 | 128 | Saturday December 2, 2006 |
| The Journal | 6 | 129 | Saturday December 9, 2006 |
| The Gaminator | 6 | 130 | Saturday December 16, 2006 |
| Graduation Day: Class of 2105 | 6 | 131 | Saturday March 24, 2007 |
| Timing Is Everything | 6 | 132 | Saturday March 31, 2007 |
| Enter the Jammerhead | 6 | 133 | Saturday April 7, 2007 |
| Milk Run | 6 | 134 | Saturday April 14, 2007 |
| Fall of Darius Dun | 6 | 135 | Saturday April 21, 2007 |
| Turtle X-tinction | 6 | 136 | Saturday April 28, 2007 |
| Race For Glory! | 6 | 137 | Saturday September 8, 2007 |
| Head of State | 6 | 138 | Saturday September 15, 2007 |
| DNA is Thicker Than Water | 6 | 139 | Saturday October 6, 2007 |
| The Cosmic Completist | 6 | 140 | Saturday October 13, 2007 |
| The Day of Awakening | 6 | 141 | Saturday October 20, 2007 |
| Zixxth Sense | 6 | 142 | Saturday October 27, 2007 |