Ascension tagline : "Deny Everything"
Duane Barry, ex-FBI, psychotic and convinced he's a multiple alien abductee, takes hostages to prevent another abduction; he wants someone else to be abducted. Mulder gets involved, becomes a hostage and, listening to Duane's detailed retelling of his experiences, believes his stories of aliens cooperating with the government; Mulder helps end the hostage situation. Duane is given the address Scully and he kidnaps her. Krycek helps Duane reach Skyland Mountain with Scully before Mulder does; Scully is taken by helicopters. Krycek kills Barry and dissappears from the FBI. Skinner reopens the X-Files.
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
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.
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."
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.
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".
"That would mean Duane Barry is
telling the truth."
"Where is she? Where'd you
X: "There are no answers for you, Mister Mulder. They only have one policy: deny everything."