When Krycek worked for the FBI, Skinner was his boss. However, Skinner did not hire him and didn't know much about him. Presumably the Consortium got Krycek hired, through one channel or another. Skinner did not seem to suspect Krycek was anything more than he seemed.
Krycek was quite deferential toward Skinner at first, as would be expected of a junior agent. When Skinner tells him to take Mulder home in "Ascension," Krycek jumps to it. And he frets when Mulder insists that they take off to Skyland Mountain without telling Skinner. However, Krycek is anything but deferential in "Paper Clip," when he and two other Consortium agents take the digital tape from Skinner. He punches Skinner out good. In the line of duty, of course. They had to take the tape, and pretty much had to leave Skinner unconscious. Skinner wasn't seriously injured, since he was back at work immediately with only a small adhesive patch on his temple to show for his ordeal. He did hold something of a grudge, however, punching Krycek in the gut in "Tunguska," even though he was handcuffed and harmless, saying, "We're not even yet, boy." He then handcuffs Krycek to the balcony rail of his 17th floor apartment and leaves him out there all night - and all day. Krycek is nearly killed because of this, and when he kills a man in self-defense, Skinner gets in a lot of trouble with a Senate Subcommittee. Richly deserved trouble, I must say.
"S.R. 819" takes the Krycek-Skinner relationship to new extremes. Krycek saves Skinner's life. A Tunisian government agent is trying to shoot Skinner - until Krycek runs him over. But there's a price to be paid. Skinner has been infected with a nanopoison, and Krycek controls it. He keeps the poison from killing Skinner...but now Skinner owes his life to Krycek. Skinner knows that one day Krycek will call in the debt.
This happens in "Biogenesis." Skinner secretly videotapes Mulder and Scully when they come to his office to report on a case - at Krycek's behest. Krycek takes the tape to the primary suspect in the case, possibly to blackmail him. Mulder and Scully suspect Skinner of betraying them, but have no idea why. They don't know Skinner is in Krycek's thrall.
In "Deadalive," Krycek contacts Skinner in the halls of the FBI building. He shouldn't be able to get in, but somehow, he did. He uses the nanobots, just to get Skinner's attention. Once he has it, he offers Skinner a cure for the deathly ill Mulder - if Skinner agrees to make sure that Scully's baby never comes to term. Skinner refuses, and Krycek leaves.
However, it's doubtful that Krycek really expected Skinner to agree to his terms. He was just taunting him. When Skinner refuses, Krycek does not threaten him with the nanobots; he just leaves. If Krycek seriously wanted Skinner to harm Scully's baby, surely he would have applied a bit more force?
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