Pastor Gideon had a daughter named Leah, who began to receive visions from "the angels" which told of the Apocalypse. He and the town began to defend against an onslaught of demon attacks with guidance provided through Leah's visions. Despite the town being in war zone, he still held church services, including weddings. He eventually recognized a fundamental difference in Leah, as her communications from the angels began to cause panic and fear in the people of his congregation.
After Paul was killed as a result of being named by Leah as one of the non-believers angering the angels enough to keep their "flock" from entering paradise, the pastor at one point grabbed Leah's arm in attempt to stop her from inciting them to further violence. "Leah" threatened to name him as one of the "sinners" if he didn't let her go. This was a sign to him that she was not his daughter.
Castiel appeared to the pastor and transported him to a meeting with Sam and Dean, and the three of them convinced him that as a true Servant of Heaven, he had to be the one to kill his daughter's impersonator, the Whore of Babylon, by impaling her with a stake made from a Babylonian cypress tree. Initially reluctant, he eventually agreed. However, he was disarmed after being assaulted by other church members, and Dean ultimately recovered the stake and made the kill.
The pastor survived the experience, albeit wounded and left to deal with the death of his daughter, who had more than likely died months earlier.