Agent Alex Krycek first had the confidence of Fox Mulder in the second season episode "Sleepless", where he plays his role of a junior FBI agent. He even adopts some of Mulder's wry wit ("Well, it puts a whole new spin on 'virtual reality'.") to try to get closer to Mulder.  We later finds out his true colours as he warns The Cigarette-Smoking Man that separating Mulder and Scully has not stopped their partnership, and that the Cigarette-Smoking Man has underestimated Agent Scully as a danger to their secrets.
The darker side of the traitor appears even more clearly in the dual episodes "Duane Barry" and "Ascension", where he plays a part in the abduction of Agent Scully and the silencing of Duane Barry. His treachery exposed, he disappears from the Bureau, only to become a greater threat than ever as he goes underground. At the end of the second season, in "Anasazi", he murders Fox Mulder's father and frames Mulder for the killing.  Mulder has no proof but suspected Krycek did it from the beginning
He is an accessory to the murder of Melissa Scully in a botched attempt on Agent Scully's life. When he ambushes Assistant Director Skinner and recovers a vital digital tape, the Cigarette-Smoking Man repays him by trying to have him killed. Krycek escapes the trap and vows revenge on his former mentor, while fleeing the country with the tape that reveals the extent of US government cover-up in alien visitations. It is not until Fox Mulder goes to Hong Kong in pursuit of another turncoat that he finds Krycek again, but this time Krycek is possessed by the black cancer.  The alien uses him to cut a deal with the Cigarette-Smoking Man, which returns the alien to his (or her) ship but leaves the ragged, terrified Alex Krycek trapped in an abandoned missile silo in North Dakota, begging to be released.
After feeding tips to Mulder on the activities of a militia group in "Tunguska," Krycek resurfaces once again to join Mulder in his pursuit of a mysterious rock. This leads them both to Russia in "Terma" where they are captured and thrown into a gulag.  Krycek is more than friendly with his captors, who seem to know him rather well. Their captors are performing experiments on the prisoners injecting their arms with a strange substance that has do with the mysterious rock that brought them to Russia. Mulder escapes from the gulag and forces Krycek come along, but they are soon separated when Krycek escapes from Mulder once again and flees into the forest. While running away he encounters a group of one-armed men that live in the woods. He tells them he is an American fleeing from the soldiers that run the gulag, and they take him in. That night, while Krycek sleeps, the men grab Krycek and cut off his arm so that the soldiers cannot experiment on him.

Krycek is next seen with a fake limb in the company of a Russian  involved with the mysterious rock. Krycek had ordered the Russian's mission and he is indeed not just the renegade agent he appears to be, but much more!!!