Though Krycek is pretending to work for Skinner when we first meet him, the mysterious Cancer Man was his real boss. In "Apocrypha," the Consortium elders refer to CM as "our associate in Washington," which suggests that the Consortium is organized along regional lines. They also refer to Luis Cardinal as "one of [CM's]." So it appears that each of the Consortium elders has his own people. Alex Krycek, like Cardinal, was presumably "one of CM's" - an operative working for the DC branch of the Consortium. Nevertheless, the other Consortium leaders, such as Well-Manicured Man, know who Krycek is - probably because of his connection to Mulder, who seems to be very important to the entire Consortium.
At first, Krycek's assignment was apparently to gain Mulder's trust while reporting on his activities to CM. But by "Ascension," Krycek was taking a more proactive role, taking action to keep Mulder from finding out things CM wished to keep secret. Nevertheless, Krycek appears to have been troubled by the Consortium's methods, if not their agenda. In "Ascension," an aggrieved Krycek asks CM, "After what you had me do?" He also presses CM about what they're planning for Scully; CM refuses to tell him, saying, "You have no rights, only orders to be carried out. You have a problem with that, we'll make other arrangements."
After the Mulder assignment is over, CM starts using Krycek as hired muscle. Krycek may have been the one who drugged Mulder's water and killed his father. He was sent with Luis Cardinal to assassinate Scully. And he and two other Consortium thugs beat up Skinner in a stairwell and took the digital tape from him.
It's obvious that CM does not consider Krycek to be Employee of the Month material, however, since he arranges for him to die in a car-bombing. But Krycek manages to escape, with the digital tape as an insurance policy. CM is forced to lie to the rest of the Consortium members, claiming the tape has been destroyed.
It's unclear why CM tried to have Krycek killed. Because he screwed up? But it was Cardinal who actually shot Missy instead of Dana - and Cardinal was not targeted by the car bomb. Indeed, Cardinal knew about the bomb, and it was his suspicious behavior that tipped off Krycek. Later, Cardinal screws up again by shooting Skinner, apparently against orders. And he doesn't succeed in killing Skinner, either. Yet he's not killed until he gets himself arrested. Perhaps CM sensed that Krycek was rebelling against the Consortium, and sought to get rid of him for that reason.
At any rate, Krycek and CM are then at cross-purposes for a time. Krycek is selling Consortium secrets off the stolen tape in "Piper Maru," and in "Apocrpyha," CM locks him in an abandoned missile silo to die. In "Tunguska," Krycek helps Mulder and Scully intercept a Consortium courier and, with the help of Vassily Peskow, completely undermines the Consortium's black cancer inoculation program.
Krycek and CM finally meet again, over two years later, in "The End." Krycek is sent to bring CM back into the tender arms of the Consortium. Curiously, when Krycek is holding CM at gunpoint, CM doesn't seem to think he has it in him to actually shoot. He taunts Krycek, saying, "Give it your best shot, Alex," then starts to turn his back and walk away.
Geez. Krycek isn't the type to hold a grudge, it seems. CM tried to kill Krycek several times. First he car-bombed him. Then he sent agents to run him off the road and shoot him (though Krycek was oilienated at the time, and might not remember). Then he locked Krycek in an abandoned missile silo to die a long, slow, painful death. And CM doubts Krycek has it in him to shoot???
This lends credence to the theory that CM turned against Krycek in "Paper Clip" because he suspected Krycek didn't have the stomach for Consortium methods. Krycek has killed before - notably the truck driver in "Tunguska" and maybe that guy in the gulag in "Patient X." But perhaps CM remembers a younger, softer Krycek. (Though all in all, Krycek is remarkably forbearing here. Most of us - including Mulder, I suspect - would be seriously tempted to shoot, under the circumstances. Or at least torment CM a little with the possibility. But Krycek doesn't.)
And it's interesting that in this scene CM calls Krycek by his first name: "Alex." Not "Krycek" or "Mr. Krycek," "Alex." (CM, if anyone, would know Krycek's real name. So maybe it really is "Alex Krycek" - or at least the "Alex" part of it.)
At the end of the episode, after CM retrieves Gibson Praise and turns him over to WMM and Krycek, Krycek offers to kill CM. WMM won't let him. CM half-expects to be shot...and seems a bit bemused as WMM's car, driven by Krycek, speeds by him harmlessly.
Goverment conspiracies, it seems, makes strange bedfellows. In "One Son," we find Krycek not only back with the Consortium, but working for CM. There's no explanation of how this came to be, or why they would trust each other. But Krycek is now doing CM's bidding, and, if you believe the script, even hoping to inherit CM's place in the Consortium. Unfortunately, CM's son, Jeffrey Spender, is standing in his way.
Krycek doesn't try to kill Spender. He doesn't have to. All he does is tell Spender the truth about his father, and Jeffrey is lost to CM forever.
In "Requiem," we find out that CM has had Krycek thrown into a "hellhole" of a Tunisian prison. He says it's because Krycek was selling something that was his (the digital tape?), but I wonder if he found out Krycek turned Spender against him, and this was his revenge.
CM, who is now a dying invalid, asks Krycek to help him retrieve a crashed UFO in Oregon, so they can start the project all over again. It's unclear whether Krycek makes a sincere effort to do this or not. In the end, he does not succeed. Instead, he kills CM, by pushing him down the chairs in his wheelchair.
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