In season two, there is an on and off appearance the Winchester brothers’ father, John (Jeffrey Dean Morgan). He is depicted as a demon hunter thirsty of revenge, determined to fight numerous personal demons.

It is in this season that the story revolves around John’s disappearance, which caused his sons to get back on hunting demons. As the brothers look for their father, they search for answers regarding the unexplainable death of their mother, as well as Sam’s girlfriend.
| Episode No | Episode Name | Directed by | Air Date |
|---|---|---|---|
| Episode 23 | "In My Time of Dying" | Kim Manners | 28-Sep-06 |
| Episode 24 | "Everybody Loves a Clown" | Phil Sgriccia | 5-Oct-06 |
| Episode 25 | "Bloodlust" | Robert Singer | 12-Oct-06 |
| Episode 26 | "Children Shouldn’t Play With Dead Things" | Kim Manners | 19-Oct-06 |
| Episode 27 | "Simon Said" | Tim Lacofano | 26-Oct-06 |
| Episode 28 | "No Exit" | Kim Manners | 2-Nov-06 |
| Episode 29 | "The Usual Suspects" | Mike Rohl | 9-Nov-06 |
| Episode 30 | "Crossroad Blues" | Steve Boyum | 16-Nov-06 |
| Episode 31 | "Croatoan" | Robert Singer | 7-Dec-06 |
| Episode 32 | "Hunted" | Rachel Talalay | 11-Jan-07 |
| Episode 33 | "Playthings" | Charles Beeson | 18-Jan-07 |
| Episode 34 | "Nightshifter" | Phil Sgriccia | 25-Jan-07 |
| Episode 35 | "Houses of the Holy" | Kim Manners | 1-Feb-07 |
| Episode 36 | "Born Under a Bad Sign" | J. Miller Tobin | 8-Feb-07 |
| Episode 37 | "Tall Tales" | Bradford May | 15-Feb-07 |
| Episode 38 | "Roadkill" | Charles Beeson | 15-Mar-07 |
| Episode 39 | "Heart" | Kim Manners | 22-Mar-07 |
| Episode 40 | "Hollywood Babylon" | Phil Sgriccia | 19-Apr-07 |
| Episode 41 | "Folsom Prison Blues" | Mike Rohl | 26-Apr-07 |
| Episode 42 | "What Is and What Should Never Be" | Eric Kripke | 3-May-07 |
| Episode 43 | "All Hell Breaks Loose, Part 1" | Robert Singer | 10-May-07 |
| Episode 44 | "All Hell Breaks Loose, Part 2" | Kim Manners | 17-May-07 |
