Scully is diagnosed with brain cancer. As Scully begins treatment alongside Penny Northern, the last survivor of the group of women abductees she had met a year ago, Mulder finds that these women were treated for infertility. With the help of the Lone Gunmen and the 'Kurt Crawford' cloned hybrids, Mulder reaches the place where the ova of the abductees are being stored. Penny dies and Scully decides to quit chemotherapy and to go back to work. Skinner starts bargaining with the Cigarette-Smoking Man for Scully's life.
This is the highly emotional episode written by 4 (!) writers (that is, Carter, Spotnitz, Gilligan and Shiban) that earned XF a nomination for an Emmy in the writing category. Even if the series could easily fall into melodrama and cheesy crying scenes, the scripts and the lead actors made it possible to tell such a heavy story in a serious, XF-special, way. Scully, being the scientist she is, deals with her new cancer in an extremely detached and calm, professional way -- an attitude that deserves respect (and not only because this is a female character of '90s TV). Well, maybe Mark Snow's music for Scully was too much. But also, for the first time, the music sounds like the soundtrack for Fight the Future (in the Lombard infiltration scene).
Abductees treated for infertility and cancer
The files at Betsy's lead Mulder to Lehigh Furnace's Center for Reproductive Medecine, where the group of surviving women abductees was being treated for infertility. This is where they learnt that their abductions had left them barren. Scully's name is referenced in this clinic's database ("This is a file directory from a federally operated fertility clinic. Agent Scully's name is on this file"), although Scully never visited. The Syndicate must have a doctor working in that clinic, opening files for every abductee.
So the abductees got barren during their abduction. The ova was "harvested during her abduction, through a high amplification radiation procedure that caused superovulation." Radiation is indeed used to render barren certain animals for population control (bees for example). But radiation is also the main cause of mutations and cancers (see Chernobyl, or plain solar radiation for skin cancers), and indeed this procedure caused the cancer as a side effect ("Barren now, from the same procedure that caused their cancer."). It seems that the appearance of the cancer coincides with the removal of the implant, it is likely the implant inhibits the cancerous cells from spreading (see 5X03: Redux II for more).
In the Lombard facility, Mulder finds the name Kevin Scanlon among other acting doctors. Scanlon is well known to Penny, he is the doctor that treated all of the group. But the MUFON women were deceived despite their caution. Kurt: "Eleven women are abducted, all with similar recollections about the experience, all developing identical brain tumors, and all refused state or federal health care because of their insistence of the facts. And all dying within the space of a year." In fact, the treatment they received did little to improve their condition and basically Scanlon followed them to their death. Scanlon's work was to keep a watch on the abductees while feeding them with false hopes of progress and remittance (Penny: "He thinks he might have isolated the cause. And that if he'd caught it earlier he might have been able to do more for her, and for me.") until they finally died as scheduled. Kurt: "And now they're left to die, their conditions hastened by the men running this project."
The Kurt Crawfords are cloned hybrids, like the Samanthas and 'Gregors' in 2X16: Colony and the young Samanthas and boys in 4X01: Herrenvolk -- Mulder identifies the the Herrenvolk boys in the green tanks as young Kurts too ("I've seen this boy before. These boys were you."). The Kurts are trying to save the women abductees, who are also their mothers. In some sense of the word. Genetically, the hybrids haven't inherited half of their DNA from their mothers, as is the common definition for a biological parent. The hybrids are created from the original (human) Kurt Crawford and alien genetic material. The hybrid DNA is then inserted into an ova obtained from these women: the ova are used "for fertilization. They constitute one half of the necessary raw materials." The ova have their nucleus taken off (the DNA is contained inside the nucleus), the hybrid DNA is then injected and the hybrid starts developing. See 2X16: Colony and 2X17: End Game for more details. Ova are frozen and stored for safekeeping in the sealed metallic vault the Kurts show to Mulder. Mulder takes a vial with some of Scully's ova; this won't be touched upon again (until season 8).
So "these women are your birth mothers." Kurt: "We're among the end results." It is true that the hybrids are used as a workforce not unlike others (Colony, 3X24: Talitha Cumi, Herrenvolk) -- here the Kurts are used as lab technicians and to create even more hybrids in the Lombard facility. But the real end result of these experiments isn't them (see 6X12: One Son) and that is why the experiments continue.
Mulder: "You've been using me." Kurt: "Not at all. Your arrival was only coincident with the execution of our objective", that is to "subvert the project. The project that created us". After the 'Gregors' and the Jeremiahs, it's clear that they hybrids have a tendency to disobey their orders -- which isn't surprising given the repetitive tasks they're assigned to. The Kurts try to save their "birth mothers" by searching the medical records and digging in databases trying to find a cure for them, a cure they know exists. The Kurt Crawfords end up being executed too, using the alien stiletto. This time however, we see no Alien Bounty Hunter: the Grey-Haired Man does the job. After 4X01: Herrenvolk and the Jeremiah Smith business, the aliens have given the Syndicate a stiletto with which the Syndicate can take care of its own menial problems internally, without having to mobilize Colonist resources; it's likely the Syndicate asked for this 'passage of power', given the value a stiletto has (Talitha Cumi).
After pointing Mulder once to the CSM's (2X08: One Breath), Skinner talks Mulder out of seeking the CSM for answers. Skinner is always in a difficult position as the middle man. He wants to keep Mulder out of the hole he's digging for himself with bargaining with the CSM. Skinner goes to CSM and compromises himself again by pleading for a cure for Scully. He knows that by this the deal he made with him in 3X02: Paper Clip on Mulder & Scully's safety is no more -- which was true anyway since Scully's life is threatened. This pact with the devil continues in 4X21: Zero Sum.
Leonard was right (4X14: Leonard Betts): Scully has cancer! We enter an extremely emotional story arc for Scully (and Mulder). Her beliefs are shaken, even though she won't admit it, and as she becomes aware of the possibility of impending death she is very candid on the log she writes in what is at that time her deathbed -- a log that is revealed to be addressed to Mulder. This culminates in the hallway scene, with a hug (and a cut kiss, which indeed could have been attributed to their emotional state, shippers take notice).
Scully's log 1 (teaser monologue): "I feel time like a heartbeat, the seconds pumping in my breast like a reckoning. The numinous mysteries that once seemed so distant and unreal, threatening clarity in the presence of a truth entertained not in youth, but only in its passage. I feel these words as if their meaning were weight being lifted from me, knowing that you will read them and share my burden, as I have come to trust no other. That you should know my heart, look into it, finding there the memory and experience that belong to you, that are you, is a comfort to me now as I feel the tethers loose and the prospects darken for the continuance of a journey that began not so long ago, and which began again with a faith shakened and strengthened by your convictions. If not for which I might never have been so strong now as I cross to face you and look at you incomplete, hoping that you will forgive me for not making the rest of the journey with you."
Scully: "What makes you think this is a conspiracy, that the government's involved?"
Kurt Crawford: "What makes you think it isn't?"
Scully's log 2: "In med school I learned that cancer arrives in the body unannounced, a dark stranger who takes up residence, turning its new home against itself. This is the evil of cancer, that it starts as an invader, but soon becomes one with the invaded, forcing you to destroy it but only at the risk of destroying yourself. It is science's demon possession, my treatment, science's attempt at exorcism. Mulder, I hope that in these terms you might know it and know me and accept this stranger some may recognize but cannot ever completely cast out. And if the darkness should have swallowed me as you read this, you must never think there was the possibility of some secret intervention, something you might have done. And though we've traveled far together, this last distance must necessarily be traveled alone."
Frohike: "The Lombard system is a dedicated mainframe. Impossible to hack. So they say."
Mulder: "Well, how'd you guys get in?"
Byers: "A modified clipper chip we cannibalized from a government surplus army field encoder."
Frohike: "We bought it back from the Chinese."
CSM: "It's funny, I always thought of you as Fox Mulder's patron. You'd think under your aegis that he wouldn't be consigned to a corner of the basement."
Skinner: "At least he doesn't take an elevator up to get to work."
CSM: "You think I'm the devil, Mr. Skinner?"
Skinner: "I'm not here to talk about what I think about you."
CSM: "Then why are you here? Is it Mulder's partner and her illness? Is it terminal, the cancer?"
Skinner: "You tell me."
CSM: "Modern medicine today, I hear they can perform miracles."
Skinner: "I need a miracle."
CSM: "Well, you think a lot more of me than you let on, Mr. Skinner."
Skinner: "What will it take?"
CSM: "For Agent Scully's life? What would you offer?"
Skinner: "What will it take?!"
CSM: "Well. I'll have to get back to you on that. Oh, Mr. Skinner, which way is the elevator?"
Mulder: "When I came to find you, you weren't in your room. I got scared that something had happened...and I read some of what you wrote."
Scully: "I didn't want you to read that. I had decided to throw it out. I decided tonight that...that I'm not going to let this thing beat me. I came into this hospital able to work, and that's how I'm leaving. [...] People live with cancer. They carry on, and so will I. You know I've got things to finish, to prove to myself, to my family...but for my own reasons."
Mulder: "Come on back." (they hug)
Mulder: "The truth will save you, Scully. I think it'll save both of us."