The FBI starts a manhunt for the missing Agent Mulder, headed by Agent John Doggett. Mulder was dying of an illness before his abduction. The manhunt leads to Arizona, where the Alien Bounty Hunter attempts to abduct Gibson Praise. Scully kills the Alien Bounty Hunter. Newly assigned Deputy Director Kersh assigns Doggett to the X-Files (in order to undermine Doggett's ascension in the hierarchy). Mulder is still missing.
The X-Files return for an eighth season, despite the expectations of the entire cast and crew during season 7. Chris Carter, on the verge of abandoning the series altogether, decides to stay and see the show he created to its end. These two episodes were written in a rush before production kicked in, and it shows in their low quality, nothing like what we've used to expect from the mythology: many long scenes, an endless boring plot of chases and escapes in the Arizona desert, virtually nothing new mythology-wise... and the elegiac "Scully's theme" by Mark Snow -- which is good by itself, but it's repeated 6 times throughout! It gets better as the season progresses though. The character of John Doggett, played by the terrific casting choice Robert Patrick, is introduced. The opening titles are changed for the first time in seven years, a longevity record for a show like this!
Season 8 pretty much rewrites the happenings of season 7, which was otherwise rather empty in mythology terms. Following the operation to transfer the alien genes from Mulder's brain to the Cigarette-Smoking Man's (7X04: Amor Fati), the CSM presented a terminal illness. Perhaps this is something Mulder would have developed in the long run if he had kept the genes. But Within reveals that Mulder developed a terminal illness like the CSM throughout season 7 but chose not to tell anybody: the operation itself was the cause. Mulder knew he was going to die. "Mulder was dying. [...] For a year, he was going to doctors. There's a clear record of his decline." He arranged for his funeral and had a tombstone made for the whole of the Mulder family, including a cenotaph for Samantha (incidentally, we are finally given the onscreen confirmation of Mulder's mother's name, and the dates of birth of both parents: 1936 for William and 1941 for Tena). He arranged this in weekly trips to his mother's grave in Raleigh, North Carolina. Retrospectively, the knowledge of his impending death was one additional reason why he went ahead with being abducted in Requiem, in hopes he might be cured (8X11: The Gift shows that he was already looking at other ways of being cured).
These episodes happen exactly after 7X22: Requiem. The cleanup of evidence from the Alien Bounty Hunter and the aliens continues, moving from Bellefleur, Oregon, to the Southwestern states. We are led to believe that the UFO we see in these episodes is the same one as in Requiem (however here it is circular, in Requiem it was triangular: an error, no doubt). Mulder is held in the ship, victim to various painful tests like any other abductee. Scully senses these tests in dreams she has; it's unclear whether these are just nightmares Scully has, or some kind of spiritual connection between the two -- as in 3X01: The Blessing Way and 7X04: Amor Fati. Gibson senses him, as well, through some kind of remote viewing due to his special abilites. Scully and Skinner go on a search for Mulder on their own, coming really very close to him, but the UFO is cloaked in an energy field. By the way, we see so many UFOs so clearly in these episodes that the sense of dread and mystery of earlier episodes (see 3X02: Paper Clip) is lost.
In these episodes, the aliens are not only after ex-abductees as in Requiem, but they gather any evidence of their presence in general: they use the shapeshifting abilities of the Alien Bounty Hunters to steal Scully's laptop, Mulder's home computer and some files in the FBI (X-Files most likely). They are also after Gibson Praise, the boy who can read minds because of the activated alien genes in him (5X20: The End, 6X01: The Beginning), indirect and living evidence of their existence: "they're removing all of the evidence before it becomes proof". Last time we saw Gibson was in a nuclear power plant in Arizona (The Beginning); somehow he got out of there (probably along with the grey alien that might have been collected by a UFO) and made his way to a school for the deaf -- a place where thought is not distorted by the vagaries of speech, a place where he could feel at home in the silence.
The Alien Bounty Hunter uses the guise of Mulder, Scully and Skinner to accomplish his mission. Not content to change forms, the ABH also changes clothes and eyewear here -- a gross mistake... Scully finally manages to kill him with a gunshot wound to the base of the neck. It was established that an alien stiletto was necessary to kill one (2X17: End Game, 3X24: Talitha Cumi, 5X14: The Red and the Black, 6X11: Two Fathers). However, conveniently enough, the contrary (that he can be killed with a conventional gunshot) was not entirely dismissed either! We could argue that the stiletto is just used so as not to release the toxic retro-virus in the 'green blood' of the ABH, which flows by the tons with a gunshot wound, but Scully shoots right on target and she and Gibson don't even feel an itch. Also, we know that the ABH is infected with Black Oil (5X14: The Red and the Black): we should have seen it here, dying along with the host (4X10: Terma). We didn't probably for the same reason we never saw the black film before the ABH's eyes: the behaviour and location of the Black Oil inside a shapeshifter's body is different from those inside a human. Just when you thought you had it all figured out, these episodes mix everything up again (are these to be considered as mistakes as well?). Back inside the UFO, we see many Alien Bounty Hunters gather around Mulder; we get the confirmation that they are many. This was to be expected, given that the clones that are not controlled by the Black Oil are part of the Rebels (5X14: The Red and the Black). This is the last time we see the Alien Bounty Hunter; his role as a Colonist under human appearance will be replaced by the Supersoldiers.
A new partnership: Agent Doggett
Agent Mulder goes missing and the FBI makes sure it does the strict necessary to find him. A manhunt for Mulder is begun and many agents are assigned to it. We meet agent Gene Crane, whom we later learn is a Supersoldier (8X20: Essence), but he doesn't appear to have helped the ABH here. We meet agent John J. Doggett, an ex-Marine and an ex-cop, a very competent FBI agent that follows the procedure and does not like unexplained items in his reports; stubborn and dedicated. "Lot of guys put you in the Director's chair one day. Which is why you've been set up to fail." We last saw Alvin Kersh in 6X12: One Son; he is promoted to Deputy Director and will become an important character for seasons 8 & 9. Kersh's friendliness with Doggett is only superficial;
Agent Doggett is partnered with Agent Scully in the X-Files. The roles are reversed: Scully has become the believer, and Doggett is the sceptic -- though not through the prism of science as a younger Scully was, but through the hard investigative method and good copwork. Scully does not tell Doggett of her pregnancy; it will take time for them to trust each other. Doggett uncovers things about Mulder he hand't told Scully, shedding doubts over Mulder and mistrust of Doggett in Scully's mind. The next episodes show the beginning of their partnership: Scully giving Mulder's trademark slideshows in 8X04: Patience, Doggett saving Scully in 8X05: Roadrunners, and Doggett having an X-File of his own in 8X07: Via Negativa (something like 1X12: Beyond the Sea for Scully). After seasons 6 & 7's lightness, season 8 returns to the darker seriousness of the origins of the show; Scully's more sober, more closed clothing reflects that. Mulder's absence is felt throughout, as he is mentioned in every episode; the same kind of always-referenced but never-seen character as Laura Palmer in "Twin Peaks" (1990-1991). In Within we get a nice wink to 2X01: Little Green Men with Scully explaining her presence in Mulder's apartment because she wanted to feed Mulder's fish!
Scully's teaser voice-over: "We live in a darkness of our own making, blind to a habitant world all but unseen by us. A world of beings traveling through time and space imaginable to us only as flights of fancy. Who are these beings we dare to imagine but fear to accept? What dark work goes on inside their impossible machines, cloaked from us by invisible forces? If they know our secrets, why can't we know theirs?"
Kersh: "This reads like a piece of pot-boiled science fiction."
Doggett: "You mean it reads like an X-File."
Scully: "What are you doing here, Agent Doggett?"
Doggett: "Keeping you apprised of the case."
Scully: "That's not your job."
Doggett: "It is, actually. And officially. I'm...assigned now to the X-Files. Whatever you and I may differ on, I'll find him, Agent Scully."