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An ex-Marine with a stern sense of duty, the Bureau's Assistant Director Walter Skinner sometimes has little patience with Mulder's unorthodox methods of investigation. More than once he has warned Mulder and Scully that their inquiries were crossing into dangerous territory. He has also been forced to shut down the X-Files, but decided to reopen them on his own authority.
Skinner seems to be caught between two agendas: agents Mulder and Scully on one side and the Cigarette-Smoking Man on the other. Frequent visits by the CSM portray Skinner as another Syndicate lackey, but his efforts on behalf of Mulder and Scully "through unofficial channels" clearly show his concern for the agents and their work. Still, Krycek has proven that the Assistant Director can never be released from the hold of those in power. The ex-Agent holds the console that can increase the amount of nanotechnology machines in Skinner's blood stream.
While he has never been fully convinced of Mulder's alien theories, Skinner is astonished to see a bright light flash across the sky and witnesses Mulder disappear in "Requiem" (7X22). He is filled with emotion as he later recounts the events to Scully. "I'll be asked what I saw," he says. "And what I saw I can't deny. I won't."