Agent Alex Krycek had wormed his way into Mulder's confidence by playing the role of the worshipful junior FBI agent to the hilt. He went so far as to adopt Mulder's wry wit to try to get closer to him. However, his true allegiance emerged when he warned the Cigarette-Smoking Man that separating Mulder ans Scully didn't stop their partnership, and that the CSM had underestimated Scully as a danger to their secrets.
The darker side of Krycek appeared more clearly when he became instrumental in the abduction of Agent Scully and the silencing of Duane Barry. With his treachery exposed, Krycek disappeared from the Bureau, and became a greater threat than ever from the underground. He later murdered Fox Mulder's father and framed Mulder for the killing.
Krycek is an accessory to the murder of Melissa Scully in a botched attempt to kill Agent Scully. After ambushing Assistant Director Skinner to recover a vital digital tape, the Cigarette-Smoking Man repays him by trying to have him killed. He escaped the trap and vowed revenge on his mentor, fleeing the country with the tape that reveals the extent of the US government coverup of alien visitations. Mulder found Krycek again in Hong Kong, only this time Krycek is possessed by the alien whose secrets he's been selling. The alien used him to make a deal with the CSM which returned the alien to his ship, leaving Krycek trapped in an abandoned missile silo in North Dakota, begging to be released.
After giving Mulder tips on the activities of a militia group, Krycek once again surfaces to join Mulder in the pursuit of a mysterious rock. Which leads them to Russia where they got captured. During captivity, Mulder sees that Krycek may not be who he seems to be. Krycek was more than friendly with the Russians, who seem to know. him very well. Mulder escaped and forced Krycek to go with him, but Krycek escaped into the forest, where he ran into a group of one-armed men that lived in the woods. He told the men that he is an American fleeing from the soldiers, and they take him in. While Krycek was asleep that night, the men grabbed him and cut off his arm so that the soldiers couldn't experiment on him. Krycek was next seen with a prosthetic arm and in the company of a Russian assassin who was ordered to get rid of all the Americans involved with the rock. Krycek was the one to order the assassin's mission, so he is not just the renegade agent he had appeared to be.
