Skinner is a former Marine and a Vietnam War veteran. In the war he once killed a boy at a very short distance, an experience which has scarred him for life. He is married to Sharon Skinner. He has been treated at a sleep disorder clinic, suffering from recurring dreams of an old woman, which may either be a hallucination arising from drug use during Vietnam or a succubus. Skinner's hobbies include jogging and boxing, the latter of which has been shown in his ability to outfight Fox Mulder and X and to defend himself reasonably well when he was attacked by Alex Krycek and his men.
Skinner took personal administrative charge of the X-Files in the latter half of Season 1, replacing Section Chief Scott Blevins. Initially, Skinner acts solely as a supervisor to Agent Mulder and Dana Scully's investigations of the paranormal. In the early episodes, it is unclear whether he is entirely independent of his actions or controlled by men such as the "Cigarette Smoking Man". Eventually, Skinner begins trusting Mulder and Scully and becomes their ally, saving both of their lives on multiple occasions. He stands up to the conspirators that tried to control him, for which he frequently pays throughout the series.
After Skinner has long broken free of the "Cigarette Smoking Man", he is again forced to take orders, this time from Alex Krycek. He is covertly infected with nanotechnology, which gives Krycek the leverage to control him. Two years later, Skinner is finally able to rid himself of Krycek, when during an attempt by Krycek on Mulder's life, Skinner fatally shoots Krycek. At Mulder's murder trial, Skinner is asked to act as Mulder's lawyer, having become a supporter of Mulder's cause. Later, Skinner and Deputy Director Alvin Kersh confront the "Toothpick Man" in Kersh's office, after Agents John Doggett and Monica Reyes discover that the X-Files office had been emptied out. This results in another, apparently permanent, closing of the X-Files division. Six years later, with the X-Files still closed down, Skinner assists Scully in finding Mulder after he goes missing while consulting on the FBI's investigation into the disappearance of a missing agent. Mulder and Skinner are shown to still be on friendly terms, despite Mulder's animosity towards the FBI for the events following the trial.
When Season 10 begins in 2016, 8 years after he assisted Scully in finding Mulder in 'X-Files:I Want to Believe' Skinner is shown to still be working at the FBI as Assistant Director. He convinces Mulder and Scully to return to active duty, and re-opens the X-Files. He sets up the meeting between Mulder and Tad O'Malley, setting up the key mythology for the season. Although he plays a limited role in this season, he appears in Babylon, reprimanding Mulder for crossing the line by using drugs. In 'My Struggle II', Skinner is present when Scully realises that Mulder is missing.