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| Aflevering | Eerste uitzending |
|---|---|
| S03E01 - (Volume Three: Villains) The Second Coming | 22/09/2008 |
| S03E02 - The Butterfly Effect | 22/09/2008 |
| S03E03 - One of Us, One of Them | 29/09/2008 |
| S03E04 - I Am Become Death | 06/10/2008 |
| S03E05 - Angels and Monsters | 13/10/2008 |
| S03E06 - Dying of the Light | 20/10/2008 |
| S03E07 - Eris Quod Sum | 27/10/2008 |
| S03E08 - Villains | 10/11/2008 |
| S03E09 - It's Coming | 17/11/2008 |
| S03E10 - The Eclipse (1) | 24/11/2008 |
| S03E11 - The Eclipse (2) | 01/12/2008 |
| S03E12 - Our Father | 08/12/2008 |
| S03E13 - Dual | 15/12/2008 |
| S03E14 - A Clear and Present Danger | 02/02/2009 |
| S03E15 - Trust and Blood | 09/02/2009 |
| S03E16 - Building 26 | 16/02/2009 |
| S03E17 - Cold Wars | 23/02/2009 |
| S03E18 - Exposed | 02/03/2009 |
| S03E19 - Shades of Gray | 09/03/2009 |
| S03E20 - Cold Snap | 23/03/2009 |
| S03E21 - Into Asylum | 30/03/2009 |
| S03E22 - Turn and Face the Strange | 06/04/2009 |
| S03E23 - 1961 | 13/04/2009 |
| S03E24 - I Am Sylar | 20/04/2009 |
| S03E25 - An Invisible Thread | 27/04/2009 |