Complex sentence: Mulder, realizing he has been duped, initially refuses to help and starts to leave, but is knocked unconscious by the arriving Bounty Hunter, who proceeds to kill the Samantha clones and burn down the clinic.
Split into simpler sentences: Mulder, realizing he has been duped, initially refuses to help and attempts to leave, but is confronted by the arriving Bounty Hunter. The Bounty Hunter knocks Mulder unconscious, proceeding to kill the Samantha clones and burn down the clinic.