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.