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Krycek with Marita Covarrubias and Fox Mulder in the X-Files office at the J. Edgar Hoover FBI Building.
In 2000, the Cigarette Smoking Man managed to have Krycek thrown into Forj Sidi Toui, a Tunisian penal colony. However, the CSM later sent Marita Covarrubias to retrieve him, when a UFO crashed in Oregon; the Smoking Man wanted Krycek to help Covarrubias to retrieve the spacecraft before Mulder could, so that the Syndicate's Project could be restarted. Krycek traveled to Oregon in search of the spacecraft, but was unsuccessful. Returning from Oregon, Krycek met up with Covarrubias and personally contacted Mulder, at FBI Headquarters, to inform him that the Smoking Man was actually dying and that the conspiracy was therefore ending with the CSM.
Krycek returned to the Watergate apartments with Covarrubias but the Smoking Man was devastated that they had failed to locate the ship, suspecting the possibility that they had never meant to find it. Krycek wheeled the CSM out of his room, while Covarrubias stopped Nurse Greta from interfering. As the two women watched, Krycek hurled the Smoking Man (in his wheelchair) down a flight of stairs. Leaving with Marita, Krycek descended the stairs and stepped over the Smoking Man's crumpled body. — (Requiem)
For nearly a year thereafter, Krycek remained out of sight and nearly out of mind. During this time, Mulder was abducted and John Doggett was assigned to the X-Files. In early 2001, Mulder's deceased body was found, having been returned from the aliens. Mulder was buried in a cemetery, although other returned abductees had been healed from this state by Jeremiah Smith, prompting Skinner to exhume Mulder and treat his bizarre condition. It was at this time that Krycek reappeared.
Krycek contacted Skinner and promised him the alien virus vaccine (which could save Mulder's life and prevent him from transforming into an alien replicant), in return for Skinner making sure that Scully's baby did not come to term. Krycek's demand appalled Skinner, who instead chose to send Agent Doggett to forcibly retrieve the vial from Krycek. In their first encounter, Doggett faced off with Krycek but Krycek merely allowed the vial to fall from his hand and shatter on the ground. Resigned to defeat, Skinner thought it best to save Scully's child and pulled the plug on Mulder's life-support equipment, incidentally halting the advance of the virus and saving Mulder's life even without the vaccine. — (DeadAlive)
Krycek's involvement with the X-Files agents was not over, however. Billy Miles began a brutal killing spree in which he murdered a number of doctors who had been working with alien DNA in fertility experiments (the victims including Scully's own doctors) and then proceeded to target Scully herself. As she and Mulder tried to escape Scully's apartment with Miles in pursuit, Krycek speedily arrived and ran over Miles with his car. Krycek drove away with the agents as Miles, mangled and bloody, managed to stand up and walk away. — (Essence)
In an unlikely meeting, the two agents spoke with Krycek and Skinner about what Billy Miles had become. Krycek explained to them how Miles had actually been replaced by an identical alien super-soldier, distinguishable only by protrusions at the top of his spine and seeming indestructibility. Scully was sequestered to a safe place with Monica Reyes to give birth, in the hope that Billy Miles would be unable to find her there. Krycek had explained that Scully's child was "special" and presented implications that threatened the entire super-soldier conspiracy.
Away from Krycek, Doggett revealed to Skinner his informant was a man named Knowle Rohrer. The morning after their escape from Billy Miles, Doggett had a secret meeting with Rohrer, leaving Skinner alone in his office with Krycek. Billy Miles then came to Skinner's office, and Krycek attempted to flee without Skinner, but Skinner managed to board Krycek's elevator at the last second. However, Billy Miles critically injured Skinner in the attack.
With Skinner in the hospital, Mulder and Doggett tried to find out more about Rohrer but were unsuccessful. As they returned to the FBI building, Mulder saw Krycek driving into the parking garage. Mulder and Doggett followed Krycek, only to discover that Krycek's passenger was none other than Knowle Rohrer. Doggett followed Rohrer into the FBI building, leaving Mulder to watch Krycek in the parking lot. To Doggett's further shock, he learned that Rohrer was meeting with FBI Agent Gene Crane. Doggett found Skinner, released from the hospital, in Skinner's office, and they phoned Mulder. After learning that Rohrer was meeting with Agent Crane, Mulder deduced that Krycek, Rohrer and Crane were involved in the alien conspiracy and were simply trying to fool Mulder, Doggett and Skinner into thinking they could protect Scully. Mulder was certain that the aliens knew where Scully was, and demanded that Doggett tell him her location so that he could get to her.
Mulder, however, had taken his attention away from Krycek, who appeared out of nowhere to smash Mulder's car window with his prosthetic arm and ripped Mulder's cell phone out of his hand. With his gun drawn on Mulder, Krycek lamented that – after years of hoping that Mulder would succeed against the alien conspiracy – he now had no choice but to kill Mulder. Mulder refused to accept any of Krycek's claims to righteousness, however, bluntly telling his nemesis that Krycek's only goal had been to save himself.
Krycek's death
At the last moment before Krycek could pull the trigger, Skinner arrived and shot Krycek. Krycek screamed and fell over as Skinner shot him again. Skinner appeared to be taking deep satisfaction in finally winning revenge against the man who had tormented him for years, most notably through the use of nanotechnology. Krycek tried in vain to grasp his weapon with his prosthetic arm and, upon failing, he attempted to convince Skinner to shoot Mulder instead. Stating that it would "take more bullets than you can ever fire to win this game," he claimed he could give Skinner a thousand lives if he were to shoot Mulder. After a brief glance in Mulder's direction, Skinner shot Krycek one last time; this time, directly in the head. Krycek uttered something inaudible after he was shot, and with his last ounce of life, turned to Mulder, keeping his eyes fixed on Mulder as he fell to ground, dead. — (Existence)
Post-Death[]
In 2002, as Mulder attempted to flee a pursuing Knowle Rohrer inside Mount Weather, Krycek appeared to Mulder, opening a steel door for him before closing and locking it on Rohrer. Despite Mulder's vocal indignation at the impossibility of this, Krycek simply told him to go, and that there were "more coming". As a result of this diversion, Mulder was able to throw Rohrer from a walkway onto electrical pylons, apparently killing him.
After Scully and Skinner left Mulder's jail cell, Mulder turned around as if continuing a conversation, at which point Krycek re-appeared. When Mulder asked Krycek why he was helping him, Krycek replied, "Because you can't do this alone." As Mulder was dragged away, he looked back and his nemesis had disappeared.
A vision of Krycek appeared exclusively to Mulder inside the courtroom while Marita Covarrubias was giving her testimony. Krycek warned Mulder that the conspirators would kill Marita if she admitted that they still existed so, when Skinner began to press her for details on the identities of the super-soldiers, Mulder insisted that Skinner instead dismiss her. He was last seen with X behind the judges, as Mulder responded to his guilty verdict. — (The Truth)
Note: Krycek's ghost does not have an artificial arm.