Agent Mulder has suffered many inflictions of pain because of his restless effort to uncover the truth. in "darkness falls" both mulder and scully become encased in a cacoon. In "Gethsemane" Scully reports that Agent Mulder was aparently dead to a self-inflicted gunshot wound. Now, Im not sure how the hell the writers are going to pull them out of this one but hey they have stunned us before. According to Most of the very vaigue "men" of the X-files Mulder is a part of the secret plan that Mulder describes as "colonizataion". this plan to colonize comes more clear in episodes such as "colony", "talithia cumi" and "herrenvolk".
Special Agent Fox Mulder is putting himself in great danger every time he desprately tries to find the TRUTH. but he is convinced that his search will lead him to it.