Following instructions left in a note by Samantha, Mulder goes to the clinic and finds several clones that look like Samantha. He is told that he was easily manipulated to protect them and that the current clones are dispensable. He follows a Samantha clone in a lab coat to an access door where another Samantha appears. Mulder is told, "She is the first. The one from which we all came. The one you must save."
Mulder refuses to assist the Samantha clones and as he walks out, he is knocked out by the alien bounty hunter. Later we see the building in a blaze. In the thick smoke, Mulder is found by a firefighter. Mulder tells him that there are women in there, but the firefighter tells Mulder he was the only one in the building. (TXF: "End Game")