Agent Mulder died late last night from an apparent self-inflicted gunshot wound to the head.
With those words, uttered by Agent Scully, the fourth season of The X-Files came to a close. In an inventive twist on the mythology arc, Chris Carter has now proposed the possibility that everything that we have seen in the past four seasons was all a hoax, a lie deliberately conceived to serve as a smokescreen on the misdeeds of the Shadow Government... and that Agent Mulder was their patsy. A brilliant move, challenging the alien-cover-up paradigm that has become too common in the series. With the next season being the final one (according to Chris Carter), this revelation can also be seen as the climax of the second act of any basic three-act story: introduction of themes and ideas, reversal of those themes and ideas, and finally resolution. "Gethsemane" served as a startling reversal to the alien mythology arc, and it will be very interesting to see how this will be resolved in September, if at all.
So the big question is: is Agent Mulder really dead? We didn't get a good look at the body at the teaser of the episode, so probably not. Only Scully would be able to identify the body, and the police would probably take the word of an FBI agent. My theory is that Mulder faked his own death, and Scully is playing along by letting the Shadow Government hear what they want to hear. This way, with the heat off of the X-files, perhaps Scully's metastasizing cancer will mysteriously 'heal'. Or perhaps it is a ploy to expose the Shadow government, who will be bolder now that the thorn in their side is apparently dead.
So whose body is in Agent Mulder's apartment? The scientist from the Smithsonian that was murdered by Shotgun man (though he distinctly had a shotgun wound in the chest)? Dana's brother (why bother to introduce him in this episode)? The informant from the Department of Defense (could have been the case if Mulder invited him over to lay low and the Shadow Government's henchmen came by while Mulder was getting take-out)? A shape-changing alien (but they usually dissolve into green goo when they die)? Whatever the case, it's going to be one long hot summer before any of this is resolved (and let's hope we don't get some cheap cop-out like Mulder mysteriously making it out of the burning train car at the end of season 2).