The episodes that changed it all. Because of Gillian Anderson's pregnancy, the writers embark on a storyline whose tenant we will discover progressively over the next years; with the first "to be continued" episodes, the mythology as we'll come to know it is born. The imagery of Mulder's vision with Scully being experimented on will be used again (3X09: Nisei, 5X02: Redux). Chris Carter was too busy directing Duane Barry that he wrote; the teleplay of Ascension was done by Paul Brown.

Duane's abductions and his visions of aliens

Duane Barry is obviously psychotic, mentally unstable as a consequence of his gunshot wound to the head. The accident in 1982 where he got this wound was "a mystery, shot by his own weapon [...] left for dead in the woods". After this, he "lost everything: wife, kids, house"; even sanity ("institutionalized on and off for over a decade"). It's safe to assume his abduction experiences began at the same time, increasing his sense of isolation when he began telling crazy stories of aliens and UFOs. His 'accident' must even have been caused by his assailants upon his first abduction, which happened in Skyland Mountain. Who would believe a mentally unstable man who took a bullet in the head?

Thus Duane's memories could very well be all delusions as Scully thinks in the beginning. But it turns out Duane's a real abductee, some of it must be real. Duane tells Mulder the government works with the aliens ("they work together with a secret cooperation", "the military, they're all in it together"). Up until now, with Season 1 and Deep Throat, we saw only hostile actions of the government against alien activities, this cooperation comes as a twist and marks the true difference between simple government, or military, and Syndicate.

In the end, black helicopters abduct Scully, but Duane still thinks it was the aliens. Even if it turns out the abductions were made by humans, there is alien activity around. Mulder notices time loss at the travel agency. Duane's drill holes in his molars "could not have been done with any of the current equipment in use", his implants in the sinus cavity and gums must be as equally difficult to place. All this points to the fact that Duane really was abducted by aliens and by humans, experimented on by both. The goals of these experiments, apart from making the abductees suffer horribly, is still unclear. The implant in his abdomen could have been easily placed with human technology. It's described as a "tracking device" and under microscope it show a microchip-like structure. It must be similar to the implant Scully discovers in her neck (3X01: The Blessing Way); Duane's implants are older and bigger since they were placed in 1982. The other two implants must be of alien origin. The barcode scanner scene in the supermarket shows this implant is also used for cataloguing and storing information.

Whether the scenes depicting him being operated are real or delusional is a question that can't be answered. It is most obvious that the aliens Duane sees are not real when he wakes up in the hospital and goes to get Scully. On one moment he fleeing as hell the aliens that appeared behind a concrete wall, and the next he's standing behind the door taking his time to come up with a plan on how to knock out the guard with the fire extinguisher. The sightings of the aliens are triggered by the implants, which are controlled from a distance and activated on a chosen moment. Certainly his mental illness helps him believe more easily these delusions. Some of his visions aren't even triggered by the implants but only come from his advanced psychosis, like the sighting of the dark suited men on Skyland Mountain, when Mulder questions him.

The Syndicate abducts Scully

Yet Mulder doesn't think Duane found Scully by tracking her down with the implant she had taken from him. "Somebody could have given him her address." Even so, Duane might still have been under the control of his implants, following their lead to Scully just as they've been meaning to lead him to Skyland Mountain since the beginning. And this lead was given to the implants by the Syndicate, by CSM more precisely. Mulder's been of some use for the Syndicate's misinformation campaign, but since 1X23: The Erlenmeyer Flask he's began seeing too much. After closing the X-Files, this really is the first hostile action of the Syndicate against Mulder: abducting Scully is the solution of the problem that CSM & Krycek talked about earlier on (2X04: Sleepless). In fact, Duane's been institutionalized for some time now and hasn't been abducted for a while. The reactivation of his implants and his whole will to take someone with him is orchestrated by the Syndicate, with the sole aim to abduct Scully. This mission completed and Duane in the hands of the FBI for more questioning, Krycek had to eliminate him. The Syndicate has power over the military too, not allowing the results of Duane's autopsy be revealed to the FBI. Since this was planned all along, X can be of no help here -- and Senator Matheson even less so. X: "This reaches beyond any of us, Mister Mulder. Even my predecessor."

Krycek's question "if Mulder's such a threat, why not eliminate him?" is a fair one. Of course we wouldn't have a series then, and CSM's answer "kill Mulder and you risk turning one man's religion into a crusade" is coherent yet not entierly believable. The real reasons of Fox's survival, much more personal, will be explored (and invented, storywise) later.

In 5X03: Redux II it is revealed that Section Chief Blevins played a key role in Scully's abduction. He was probably the one that eased Krycek's actions as a double agent, or pointed Duane to Scully, or assigned Mulder & Krycek on Duane's case in the first place; or his role could have been outside of his FBI field of action altogether. Whatever it was, it can't be seen from these two episodes.

Double agent Krycek

Krycek's orders were to gain Mulder's trust but at the same time allow Duane reach the top and let Scully be abducted. When Mulder took the tram up, Krycek had to slow him down. Mulder was having success at escaping from atop the tram and Krycek had to power it up again in order to keep Mulder constrained on the tram ("I'll hold him until you advise"). But in doing so, the tram reached its destination and Mulder got to Duane. On top of this, Krycek had to dispose of the tram operator. Krycek didn't handle this particularly well.

Krycek wasn't supposed to leave the FBI so soon: "you've earned [Mulder's] trust, the object now is to preserve it", "until [Krycek's] assignment is complete" (CSM). Krycek's immediate task was to corroborate Mulder's story on the death of Duane, so that Mulder doesn't get the blame for this death against appearances. But Mulder is faster than expected and is sure to blow Krycek's cover. Krycek's last assignment as woud-be FBI agent is to save Mulder from being accused of Duane's murder; with Krycek gone, the death of Duane remains unresolved and the FBI faces a dead end.

Character development

In these early episodes it's so painfully obvious how frustrated Krycek is with being so low on the hierarchy. After failing to shake hands with M&S, CSM treats him very poorly: "we tell you only what you need to know [...] you have no rights, only orders to be carried out". This announces his rebellion in 3X02: Paper Clip and his progressive rise in power.

Finally, after some episodes where Skinner appeared as cold as CSM, Skinner uses his own authority in the FBI to go against the Syndicate: he reopens the X-Files, "that's what they fear the most". CSM is seen lurking and smoking in Skinner's office time and again, but Skinner isn't manipulated as easily as Blevins, or at least he isn't that deep into the Syndicate. Blevins is higher up the hierarchy of the FBI than Skinner, and by acting on his own free will, Skinner must have limited his carreer prospects. CSM will always have some trouble getting Skinner to do what he wants.

We see Margaret Scully again, after 1X12: Beyond the Sea. She still calls Mulder "Agent Mulder".

Duane Barry

Duane Barry: "I just want to go back to the place."
Mulder: "What place?"
Duane Barry: "Where it first started. Where they first came and got me."
Mulder: "Where is that?"
Duane Barry: "A mountain. We went up... and up. Ascending... ascending to the stars."

Mulder: "That would mean Duane Barry is telling the truth."
Scully: "Or some version of the truth."

Ascension

Mulder: "Where is she? Where'd you leave her?"
Duane Barry: "They took her."
Mulder: "Who?'
Duane Barry: "Them!"