While Doggett was in some ways even more of a skeptic than Scully was when The X-Files began, he wasn't a hard character to like, as even though he was predisposed to skepticism, he readily cared about Scully's well-being, and would never totally dismiss her theories. One thing he did have in common with Mulder is a tragic personal loss. Whereas Mulder had his sister Samantha, who he believed had been abducted by aliens, Doggett was tormented by the loss of his son Luke. While he knew what happened to Luke, as his dead body was found, for many years, he didn't know why, and it ate away at him.
Finally, in the season 9 X-Files episode "Release," Doggett learned the whole story behind his son's disappearance and death. It's horrifically awful, and hurt to hear, but it at least helped Doggett and his estranged wife get some closure on what happened.
X-Files: What Happened to Doggett's Son Luke
In "Release," episode 17 of The X-Files season 9, an FBI cadet named Rudolph Hayes ends up steering Doggett down the path to finding Luke's killer. Of course, that's because his real name is Stuart Mimms, a former mental patient with a possible psychic ability. Mimms is briefly accused of the crime, but eventually ruled out. It turns out Mimms' information was correct. Luke Doggett was abducted by a pedophile named Robert Harvey, as he was out riding his bike. Harvey had been a suspect at one point, but they couldn't prove he did it.
However, it wasn't Harvey who killed Luke. A mobster named Nicholas Regali, who worked with Harvey, walked in on him molesting the child, and Luke looked him in the eyes. Not wanting to be associated with Luke's abduction and assault were the boy to be set free, Regali murdered him. Doggett came close to shooting Regali once he found out the truth, but Regali's scorned former FBI associate Brad Follmer did the deed first. With Luke's killer dead, Doggett and his wife Barbara reunited to scatter their son's ashes into the sea. Luke's death may not have been an X-File, but the man behind it was definitely a monster.