Mulder and Scully's X-Files boss Walter Skinner (Mitch Pileggi) is a normally trustworthy character among liars, but his origin story is quite tragic. Skinner began his tenure on The X-Files in an odd position, assigned to oversee The X-Files office specifically as an FBI Assistant Director. While at first appearing a bit antagonistic to Mulder and Scully, it wasn't too long before it was clear that Skinner was one of the few FBI employees not willing to sacrifice all ethics to serve the Cigarette-Smoking Man's whims.
At times though, he probably wished he was a little less loyal, as standing up for and protecting Mulder and Scully sometimes got Skinner in trouble with his superiors, making it a wonder he's still at his post by the time the 2016 X-Files revival begins. Skinner went to bat for Mulder and Scully when no one else would, and for that, he earned their mostly undying loyalty. It's only mostly due to a few instances where Skinner was forced to play both sides a bit in order to avoid not getting his own goose cooked.
While Skinner's no doubt a good, decent man at heart, that was shaped by some rather horrific experiences in his youth. Before he could become the man he became, Skinner went through the hell of war.
X-Files: Walter Skinner's Surprisingly Tragic Origin Story Explained
For most of The X-Files' run, Walter Skinner's past was fairly mysterious. Fans rarely saw him outside of the office, and even more rarely outside of him directly working for the FBI. It wasn't until season 11's "Kitten" that Skinner even got his biggest focus within a single episode. "Kitten" reveals a horrifying experience that Skinner had during his tour of duty during the Vietnam War.
Skinner had volunteered to serve in the Marine Corps at 18-years-old, believing it the right thing to do, but returned home a distraught shell of his former self. This was partly due to witnessing the titular character slaughter civilians after being purposefully exposed to a biological weapon called MK-NAOMI, created by the U.S. government to make soldiers more violent by tapping into their fear response.
As if that wasn't bad enough, Skinner recounts in the much earlier "One Breath" another terrible Vietnam event, in which he had been forced to shoot a 10-year-old Vietnamese boy who walked into his unit's camp covered in grenades. These war experiences scarred Skinner on a deeply personal level, and at the end of "Kitten," he would actually reveal to Mulder and Scully that despite his backing of them preventing a rise through the FBI's ranks, the duo's dogged pursuit of the truth had restored his faith in humanity and willingness to push back against the dark forces that really control the government.