| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Ben 10,000 | 3 | 27 | Saturday November 25, 2006 |
| Midnight Madness | 3 | 28 | Saturday December 2, 2006 |
| A Change of Face | 3 | 29 | Saturday December 9, 2006 |
| Merry Christmas | 3 | 30 | Monday December 11, 2006 |
| Benwolf | 3 | 31 | Saturday February 17, 2007 |
| Game Over | 3 | 32 | Saturday February 24, 2007 |
| Super Alien Hero Buddy Adventures | 3 | 33 | Saturday March 3, 2007 |
| Under Wraps | 3 | 34 | Saturday March 10, 2007 |
| The Unnaturals | 3 | 35 | Saturday March 17, 2007 |
| Monster Weather | 3 | 36 | Saturday March 24, 2007 |
| The Return (1) | 3 | 37 | Saturday April 7, 2007 |
| Be Afraid of the Dark (2) | 3 | 38 | Saturday April 14, 2007 |
| The Visitor | 3 | 39 | Saturday April 21, 2007 |