So Mulder’s dead and Scully’s crying about it. But we know better. We start this episode knowing that Mulder and Scully are going to play the lying, deceitful game the government are playing. Moments before Mulder ‘apparently’ shoots himself, he’s contacted by Michael from the DOD informing him he’s under surveillance. Instead of tossing his apartment over for the second time, Mulder notices the camera on the roof and heads upstairs to see what’s the matter.
There he finds some other DOD guy spying, words are exchanged and a shotgun blast goes off. We don’t see what happens until Mulder meets with Scully after she’s told everyone he’s dead. The guy in Mulder’s apartment is the dead DOD guy – and Mulder’s asking Scully to make them believe the lie – that Mulder is dead. Skinner finds out about this and isn’t too happy. However Scully wants to prove to people that she’s involved in something more then just debunking Mulder’s work. Meanwhile, while supposedly dead – Mulder can peruse his own interests. Believing that everything in his life is just a hoax – he sets out to fix the one thing that may be his fault… giving Scully crazy cancer. So with the dead guys credentials, he enters the DOD, finds Michael who explains his reasons for helping Mulder.. (his son is suffering from coming back from the gulf war), he manages to find his way into a lab filled with bodies on tables… the bodies look alien. Another room shows people on beds, exposed to flashing lights and sounds – similar to that of an alien abduction.
It’s important to remember what Michael told Mulder – That after the world wars, and the development of the atom bomb, the American public needed their attention taken away from the lights of Hiroshima.. so the government fabricated the story of Roswell.. from then, the story went on it’s own – abductions, sightings etc… all of which helped make the public forget that the government was still at war, developing weapons, super sonic aircraft – and biological weapons. The ‘alien abductees’ were taken not by aliens.. but by their own government. Mulder manages to find his way into the Pentagon, the same room we see the Smoking man enter at the beginning.. kind of like an evidence locker. It’s when Mulder leaves this room, we see the Smoking man discover Mulder is still alive. He met with the mono-tone sounding guy from the security council to ask why Mulder was under surveillance, but had no answer. Scully however knows the man watching Mulder was contacting Skinner.
Scully gets results from the ‘alien’ samples found in the mountain (which Michael stated was fake), and she found unclassifiable DNA inside. After testing it with her own DNA, it was a match – This means Scully has been infected with the same substance that the government are using to create these elaborate hoaxes or is it alien? Just before she can tell an FBI committee that Skinner was involved in this conspiracy somehow… she faints (remember, the DOD agent spying on Mulder made calls to an extension Skinner has access to, but we don’t know Skinner received those calls). Mulder thinks he found Scully’s cure in the Pentagon – but the Lone gunmen inform him it’s simply water.
Everything seems to be back at square one. So to summarise.. Mulder is ‘dead’, only Scully, Skinner and Smoking man know, Scully fainted but believes Skinner is really bad, and Samantha is no closer to home just yet ;)