When we last saw Alex Krycek, he was driving Mr. Well-Manicured Man. Luckily, he wasn't doing chauffer duty during the X-FILES movie, when WMM was killed in a car explosion. Presumably, though, Krycek's connection with the Consortium died with WMM. He seems to be out on his own again.
In "S.R. 819," Krycek appears to be an agent of the Tunisian government. Someone in the U.S. government wants to export nanotechnology - mechanisms of microscopic size - to Tunisia. The export of such cutting-edge technology is illegal, for security reasons. But the politically-connected Senator Matheson is in on it, and it looks like Senate Resolution 819 is going to go through, pending routine security clearance from the FBI, in the person of A.D. Skinner. Until a world-famous physicist, Dr. Orgel, tries to contact Skinner and warn him.
Someone stops Dr. Orgel, infecting him with the nanomechanisms, perhaps as a warning to Senator Matheson. (At one point, it appears that Krycek, who can control the nanopoison, kills Orgel, but by end, we don't know if he's really dead or not.) Someone gives Skinner the same poison - perhaps Krycek? At any rate, Krycek phones Skinner and tells him that he has 24 hours to live.
Yet Krycek doesn't want Skinner to die. When a Tunisian agent tries to kill Skinner, Krycek kills the man, saving Skinner's life. And at the very end, when it appears Skinner is dead, Krycek turns off the poison and revives him. It appears Krycek has betrayed Tunisia, just as he betrayed Russia.
Skinner recognizes who saved him (despite Krycek's disguise, an "expensive wig" and fake beard), and does not report it. Nor does he allow Mulder and Scully to continue the investigation. And three weeks later, when Skinner is fully recovered, he is unsurprised to find Krycek waiting in the back seat of his car. "What do you want from me, Krycek?" Skinner asks. "All in good time," Krycek replies.
So now it appears Krycek has a hold over Skinner: his life is quite literally in Krycek's hands. Was that his intent all along? Did he want to save Skinner's life? Persuade him to help Mulder more? Just annoy the Tunisians? Krycek's motivations are murkier than ever.
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