The Consortium has been destroyed, but Krycek still survives, and is still following his own agenda. Apparently using the nanotech threat, he gets Skinner to give him information about the case Mulder and Scully are working on. And he kills Sandoz, who is about to decode an important alien artifact. (It looks like he kills Sandoz, anyway. We don't actually see him do it.)
Krycek makes another brief appearance in "The Sixth Extinction II: Amor Fati." Scully catches asssaulting Skinner, but he escapes through the crowded halls of the FBI building before she can catch him. Later, we see him at Kritschgau's apartment, Kritschgau is dead on the floor. Krycek burns some documents, then leaves with the apartment in flames, taking Kritschgau's laptop with him.
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