| Title | Season | Episode # | First Aired |
|---|---|---|---|
| Traction | 1 | 2 | Saturday September 25, 2004 |
| 8 | 1 | 8 | Saturday November 20, 2004 |
| A Dark Knight to Remember | 3 | 29 | Saturday October 1, 2005 |
| A Fistful of Felt | 3 | 30 | Saturday October 8, 2005 |
| A Matter of Family | 4 | 40 | Saturday September 23, 2006 |
| A Mirror Darkly | 5 | 57 | Saturday November 3, 2007 |
| Artifacts | 4 | 46 | Saturday February 3, 2007 |
| Attack of the Terrible Trio | 5 | 61 | Saturday February 2, 2008 |
| Batgirl Begins (1) | 3 | 27 | Saturday September 17, 2005 |
| Batgirl Begins (2) | 3 | 28 | Saturday September 24, 2005 |
| Bird of Prey | 1 | 11 | Saturday February 12, 2005 |
| Brawn | 3 | 32 | Saturday November 12, 2005 |
| Call of the Cobblepot | 1 | 3 | Saturday September 18, 2004 |
| Cash for Toys | 3 | 35 | Saturday February 4, 2006 |
| Clayface of Tragedy (2) | 1 | 13 | Saturday May 7, 2005 |
| Clayfaces | 4 | 42 | Saturday October 7, 2006 |
| Fire | 2 | 16 | Saturday May 28, 2005 |
| Fleurs du Mal | 3 | 34 | Saturday November 26, 2005 |
| Gotham's Ultimate Criminal Mastermind | 3 | 39 | Saturday May 13, 2006 |
| Grundy's Night | 2 | 24 | Saturday August 27, 2005 |
| Joker Express | 5 | 58 | Saturday November 10, 2007 |
| JTV | 2 | 21 | Saturday July 9, 2005 |
| Lost Heroes (1) | 5 | 64 | Saturday March 8, 2008 |
| Lost Heroes (2) | 5 | 65 | Saturday March 8, 2008 |
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