Krycek disappears during "Ascension." We don't see him until about 8 months later. And he's changed. No longer professional-looking in a geeky sort of way, he's traded in his suits for a black leather jacket and jeans. His hair is much longer, and he doesn't seem to be very happy.
In "Anasazi," Mulder's father appears to be about to tell Mulder the truth. He goes to the bathroom to take some medication first, and we see Krycek standing in the shower, reflected in the mirror of the medicine cabinet. We don't see what happens next, but there's the sound of a gunshot, and when Mulder runs into the bathroom, his father is lying on the floor, pills scattered around his body. The bathroom is otherwise empty. The window is open, however, and we hear the sound of a car starting and driving away quickly.
Krycek later tells Mulder he didn't kill his father. He could have been lying. He could mean that CM or whoever gave the order is the real killer. He could mean that Bill Mulder wasn't Mulder's real father. Or...he could be telling the truth. We still don't know who actually killed Mulder's father. Perhaps he killed himself. Or some other Consortium operative might have been there, and been the actual triggerman.
Later in "Anasazi," we see Krycek again when Mulder catches him sneaking around outside his apartment. Mulder, who is half-crazed from drugs being put into his water, beats Krycek severely and would have shot him if Scully hadn't appeared and shot Mulder first.
We never find out why Krycek is sneaking around Mulder's apartment that night. If he was sent by the Consortium, to poison Mulder's water or spy on him, he's a suspicious choice. They know Mulder is paranoid, and likely to be even more so, now that he's drinking doctored water. So why send someone Mulder is likely to recognize on sight? Perhaps CM hoped that Mulder would catch Krycek -- and kill him. Mulder would end up in jail, and the truth would be safe from him once and for all.
If CM didn't send Krycek to Mulder's apartment that night, why did Krycek go there? Did he hope to talk to Mulder about something?
In "The Blessing Way," Krycek appears again. This time, he is waiting in Scully's apartment with Luis Cardinal. They have been sent to kill her. Cardinal has been sent for that purpose, anyway. It appears that Krycek was hiding around the corner -- in no position to shoot, even if he wanted to. Cardinal shoots the wrong person, however, hitting Scully's sister Melissa instead. Krycek is distressed when he sees it's Melissa, while Luis doesn't seem to realize she's not the right woman, so perhaps Krycek was along to tell Luis which one was Scully.
In "Paper Clip," Krycek, along with Luis and another man, accost Skinner in the stairwell at the hospital where Melissa is being treated. They beat him up and take the digital tape which he took from Mulder's desk. Later, the three stop at a convenience store. Luis says he's going to get some beer, and asks Krycek if he wants anything. Krycek, distracted and brooding, refuses. Luis offers again, is again refused, then leaves with the other man. Krycek seems to find something odd about Cardinal's solicitude. He looks around and sees his two colleagues hanging around at the door of the store, watching as if they're waiting for something to happen. Then he looks down and sees the clock on the dashboard of the car blinking "12:00." He realizes then that he's been set up, jumps out of the car, and runs like hell. It explodes behind him, leaving the other two Consortium thugs to fume at his escape.
CM is the clearly one who ordered Krycek killed. When Krycek calls him up, CM is surprised that he's still alive. Krycek has the digital tape, and warns CM that he'll expose all if they try to come after him.
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