Not much is known about Doggett's past. His birthdate is April 4th, 1960. He worked at the NYPD for 7 years and had a son named Luke, who had been murdered. Doggett tells Monica Reyes in Empedocles that if he accepted the paranormal events as real, than there would have been something else he could have done to save his son, and he did't want to believe that.
Doggett officially(he had been working with Scully while Mulder was away) replaces Mulder when Mulder quits the FBI in Vienen. Doggett is protective of both Scully and Reyes. Scully, as his friend, and Reyes as maybe something more. In Audrey Pauley, Doggett laments over not kissing Reyes while she is near death. In Release, Doggett's ex-wife tells Scully that Doggett and Reyes could have something, but he won't 'let her in.' Finally, in Sunshine Days, while standing in the hospital, Reyes takes Doggett's hand, a very subtle, but very meaniful gesture.
After Agent Scully leaves, Reyes replaces her on the x-files. She and Doggett work together until The Truth, when the x-files are shut down yet again.