| Title | Season | Episode # | First Aired |
|---|---|---|---|
| The Batman vs. Dracula | 3 | 26 | Tuesday October 18, 2005 |
| Batgirl Begins (1) | 3 | 27 | Saturday September 17, 2005 |
| Batgirl Begins (2) | 3 | 28 | Saturday September 24, 2005 |
| A Dark Knight to Remember | 3 | 29 | Saturday October 1, 2005 |
| A Fistful of Felt | 3 | 30 | Saturday October 8, 2005 |
| RPM | 3 | 31 | Saturday November 5, 2005 |
| Brawn | 3 | 32 | Saturday November 12, 2005 |
| The Laughing Cats | 3 | 33 | Saturday November 19, 2005 |
| Fleurs du Mal | 3 | 34 | Saturday November 26, 2005 |
| Cash for Toys | 3 | 35 | Saturday February 4, 2006 |
| The Apprentice | 3 | 36 | Saturday February 11, 2006 |
| Thunder | 3 | 37 | Saturday February 18, 2006 |
| The Icy Depths | 3 | 38 | Saturday May 6, 2006 |
| Gotham's Ultimate Criminal Mastermind | 3 | 39 | Saturday May 13, 2006 |