In 2000, Doggett was the leader of a task force organised by FBI Deputy Director Alvin Kersh with the sole purpose of searching for Fox Mulder, who had gone missing in Bellefleur, Oregon.

Shortly after the search began, Doggett took statements from Mulder's partner, Special Agent Dana Scully, and his superior officer, Assistant Director Walter Skinner. Doggett reported the statements to Kersh but omitted AD Skinner's claim of having watched Mulder being abducted by a UFO, believing that alien abduction was extremely unlikely and seeing no way in which that account could help find Mulder.