The X-file here is the visions of Skinner, the red-coated old woman that seemed menacing to Skinner but by the end proves to be something like a guardian angel. Skinner's near-death experience was introduced in 2X06: Ascension; his visions had started then, in a Vietnam ambush. They began again when Skinner's carreer and life was in danger, about after 3X15: Piper Maru when he was shot ("Skinner has been receiving treatment for the past three months", "A few months ago, I started seeing her again") and suffered from his marriage (well, its failure). Such visitations of a "succubus" are known since the middle ages according to Mulder. The old woman gives Skinner the location of the Syndicate henchman speaking through Sharon Skinner, which permits Skinner to get to him and kill him. It looks like Walter & Sharon get back together at the end, but in 4X09: Tunguska we find Skinner in yet another apartment, alone again.

After a failed murder attempt on Skinner (Piper Maru), CSM tries to solve the inobedience problem at the FBI by forcing the FBI to fire Skinner. Scully: "Why not just kill him?" Mulder: "Well, they already tried that once, and a second attempt would be too obvious, even for these thugs. Anyway, I think Skinner's probably worth more to them alive in disgrace than dead and buried." We already saw both of the Syndicate men present here in action before: they and the Grey-haired Man were the ones that gave Skinner a warning in the café in Piper Maru. The Grey-haired Man seems to be higher in the hierarchy since the other one does all the dirty work. All the other FBI agents and elders we meet (Agent Bonnecaze and the Senior Agent) don't need extra lobbying from the Syndicate to mount a case against Skinner, his guilt seems obvious enough thanks to CSM's schemes.

A cut scene between CSM & Skinner offers more insight (with juicy and straightforward dialogue): CSM: "You're in an untenable position. I'm here to offer my assistance." Skinner: "Out of what? Professional courtesy?" CSM: "On old favors. Which gives me leverage to influence certain outcomes."

Decidedly, CSM has a lot of trouble making Skinner blindly follow his orders. Skinner has always walked the line through the years (6X10: S.R.819).