From the moment Mulder stumbles into his apartment, he and Scully are joined as the two halves of one mind, operating as left and right hands of a single purpose. Even when they argue in front of the Well-Manicured Man, their disagreement is of a fundamentally different nature than their argument outside the hospital in the series pilot. Scully is no longer dismissing the idea of alien abduction out of hand, she is simply disagreeing with the evidence presented. Mulder's transformation is profound: he not only leaves the decision over the tape to Scully, he does not even present his arguments to her. He knows she knows him well enough to know what he would say. His trust in her is complete; she has been drawn permanently into the sacred circle of his faith and hope. Scully is now part of the quest, which has become as personal and real to her as to Mulder.
The theme of "Paperclip" is really about choices. The choices Bill Mulder made, the choices Deep Throat made, and now the choices Mulder and Scully make, are the ultimate expression of humanity. Only humans choose. All else obeys the invisible dictates of instinct, and probability. The point of a heroic quest is to bring back a truth that holds up a mirror to our souls. Mulder and Scully could choose to quit, or to be intimidated, or to go rogue and run from the Cigarette-Smoking Man for the rest of their lives. But they choose to return to the X-Files, to the basement office, to the pursuit of elusive cases bounded by hostility and frustration. It is difficult, and daunting, and dangerous. This is the path of harmony, the path of Beauty that takes them clear-eyed and aware into the heart of darkness, on a hero's journey.
The only flaw in this arc is the lack of connecting emotion between the various characters. Except for Margaret Scully, and the final scene between Mulder and Scully in Melissa's hospital room, there is very little expression of emotion in this arc. There's plenty of awesome action when Mulder confronts Krycek, or when the Cigarette-Smoking Man tries to bully Skinner. But when Scully thinks she's lost Mulder to a hideous death, when Mulder is brought back from death by Albert Hosteen, when Mulder meets his mother for the first time since his father's murder--these scenes are too emotionally muted. Drama is first and foremost about emotion. I could have used a little more of it in those scenes. The puzzles are interesting, vital to the show, of course. But I find it difficult to connect with a Mulder who cannot even thank Albert for saving his life, who cannot comfort his mother, who takes Scully so much for granted he cannot even say "Did you miss me?" when he returns from the dead. If she shows so little of her inner reactions to us when her life is being irrevocably changed, how shallow will her reactions be to an "ordinary" X-File?
Beyond the changes implicit in the character development in this arc, we see other tectonic shifts taking place. Skinner finally decides where his loyalties lie, and the Smoking Man loses some of his threat. It's hard to be scared of a man who is visibly shaken. Mulder learns that his sister was sacrificed for him and Scully learns that her sister died in her place, burdens of guilt that could easily warp strong souls.
Duchovny gives us a wonderful moment of body language when Mulder stands silhouetted against the rising lights of the mothership, caught literally like a deer in the headlights, echoing fear and wonder. The dance of firelight and shadow on Mulder in the hogan, the sooty atmosphere of the Smoke Ring's clubhouse, and the nearly silent stampede of aliens past Scully in the mine shaft make these scenes classics of composition and execution.
