Tagline of Part II: "Nothing Important Happened Today"
Under the new Supersoldier threat, Mulder has to go into hiding. Scully discovers that William is not as normal as it seems. Doggett brings Reyes in the X-Files. Two of Doggett's friends from the Marines turn out to be Supersoldiers. The new X-Files investigate a top secret program to trigger pregnancies and the creation of organic versions of the Supersoldiers through a modified version of chloramine added in the public water supply.
The X-Files return for a ninth season despite, again, the wishes of the TenThirteen people. At the last minute, Carter accepts to return rather than see somebody else given the helm and the scripts are written in a rush right before production kicks in. This time, Carter doesn't handle the season opening alone as he used to: Frank Spotnitz joins the party. The opening credits are given a heavy lift and remix (including an attempt to keep fans watching by including their online nicknames...). Monica Reyes becomes a regular and in the process loses that quirckiness that made her character interesting in season 8. After so many years of service, Mitch Pileggi finally gets credit as a regular. Brad Follmer is introduced and Alvin Kersh's importance grows. This is no longer a two-lead show, no more trademark believer/sceptic opposition, this has become an ensemble show. A great part of these episodes is evidently filler time: internal politics of the FBI, scheming of one Assistant Director over another, alliances made... We even get out-of-character dialogue (Scully to Doggett: "I'm going to ask you to leave. I'm going to ask you to leave and not come back here.") and a forced explanation as to Mulder's (well, Duchovny's) absence.
Despite Duchovny's departure, Anderson stays behind. The show is changing, and maybe not in the best way possible: the focus, again, is Scully's baby and Mulder going missing. Might it not have been better to make a clear cut and reboot the series in a different form (spin-off)? Better yet, do that from season 8? The world is changing as well: by the time the episodes air, the September 11 2001 attacks have come to pass, essentially ending the decade of the 1990s, to which the mythology of the X-Files was closely tied to. The time has come to turn over a new leaf...
Shannon McMahon was introduced with the purpose of making her a recurring character (but that didn't happen in the end). With Rohrer having lost Doggett's trust, McMahon does what she can to gain Doggett and the X-Files' trust -- even stage her own (fake) death by Rohrer's hand to stress that she and Rohrer belong to different sides. Nice wink to a show to which the X-Files owes much, "Twin Peaks" (1990-91): McMahon is from Snowqualmie Falls, where "Twin Peaks" was shot!
Doggett was in the Marines, Bravo Company, in 1977-1983 (8X01: Within); here he tries to track back all his old Marine mates and, what a coincidence, two of them are Supersoldiers! (maybe more since he can't find them all) "Knowle Rohrer and I were drafted right out of Bravo Company together."
Oddly enough, 8X18: Three Words implied that only certain people with a specific genetic profile could be replicated; what are the odds that two of them would be from the same Marine Company? Perhaps what McMahon is referring to with "seven stages advanced in the science which created me" is research to convert not only these people, but anyone into Supersoldiers. Then those who were initially chosen for replication were because of their potential for infiltration in high seats of power. With the Syndicate gone, in 7X22: Requiem a new phase started: mass replication in the final phases before colonization ("there are many more now"). And The Syndicate knew nothing of this. "I'm a bio-engineered combat unit. I have no weaknesses. I don't sleep. I can breathe underwater." "We can't be killed." "Physically, she seems absolutely normal"; nothing but a "standard mutation", "a small deformity of the spine" betrays their true nature.
The chloramine project: organic Supersoldiers
McMahon explains that the Supersoldiers program is still actively doing research: "Now there are seven stages advanced in the science which created me, to the point where now they've successfully given birth to a Supersoldier from a mutated egg." This top secret research is what was conducted on the ship Valor Victor, which was stationed at large so that the risks of information leak woud be minimal ("spends 12 months a year at sea"). The scientists there were "manipulating ova, females eggs for transplantation"; the obvious source for these ova is from the abductees in a program initially conducted by the Syndicate (4X15: Memento Mori).
What the Valor Victor achieved was a means to trigger the creation of an entire generation of babies that would become Supersoldiers: organic Supersoldiers! "To prime a population to breed a generation of Supersoldiers." This would be achieved thanks to a modified version of chloramine. "Chloramine is just a substitute for chlorine. You can drink it and it's harmless." It's a "government additive" that is put in the water supply in water treatment plants to prevent the water to be infested by bacteria in the long run, a persistant disinfectant. Chlorine was traditionally used for this purpose (which gave water that blue-ish tint), now progressively replaced by the more stable chloramine (which gives a green-ish tint). The quantities and the water quality are regulated by the Environmental Protection Agency (EPA). "If you want to deliver something to everyone's home in America what better way than through what's most taken for granted: water!" Once again, the X-Files very successfully make something terrifying out of an everyday issue! Chloramine is a simple chemical (NH2Cl) but it can be modified to carry organic groups (the R in R2NCl), and it's one of these forms that the Valor Victor was trying to create: "Chloramine base T-4" (Doggett finds that name in the water reclamation plant files). This organic group is a modified version of the Black Oil virus that was used to transform grown humans into Supersoldiers (DeadAlive).
After the fertilization and birth, a continuous supply of modified chloramine through the water (drunk by the mother and then the child) progressively brings about the conversion from what is a normal human baby into an 'organic Supersoldier', slowly building up a metal vertebra and eventually an alien consciousness. The precision 'organic' in 'organic version of a Supersoldier' is not random and has a significance: the 'classic' Supersoldier is created after elaborate and painful experiments in a mechanical environment (Scully's dreams in 8X01: Within, 8X15: DeadAlive); the 'organic' Supersoldier is created much more smoothly after gestation in a mother's womb. Again, the same sentence explains everything: "successfully given birth to a Supersoldier from a mutated egg": the babies are to become Supersoldiers.
The Valor Victor, William and Mulder
Three people involved in the chloramine project have second thoughts and decide to go public with the top secret program ("they were killed because they wanted to expose the program"). The one is Carl Wormus, "Deputy Director of the Environmental Protection Agency", drowned by McMahon. The second is Roland McFarland, worker in the Greater Maryland Water Reclamation Facility, also drowned by McMahon. They had contacted McMahon in the Department of Justice "as whistle-blowers", unaware that McMahon was actually a Supersoldier herself. The third man is the Captain of the Valor Victor, but McMahon and Rohrer were not able to identify him. They used Doggett and the X-Files to get to him: Reyes: "there's still one man she can't pinpoint and she wants you to lead her to him". With Doggett under investigation by the FBI, McMahon hides Wormus body at the critical moment when Follmer was about to discover Doggett and Reyes were conducting illegal autopsies; McMahon wants Doggett to continue his investigation. The Supersoldiers' suspicions are confirmed with the Captain's call to Wormus, intercepted by the Lone Gunmen (the Captain, out at sea, was unaware of Wormus's death). Rohrer boards the Valor Victor undercover and eventually decapitates the Captain. The nature of the Valor Victor having been compromised, Rohrer decides to blow it up so that Dogget and company don't discover anything more.
In 48 hours, Mulder had the time to become a father, to guest star in an episode of "The Lone Gunmen", and to take one of the most difficult decisions of his life: to leave Scully and William. Scully 'explains' that "he can't be brought back into this, he can't be brought back to the FBI, it's just too dangerous for him right now". Even if this feels extremely artificial to accomodate Duchovny's departure from the show, the reasons behind this are that the Supersoldiers want Mulder dead. Kersh: "I told Mulder that he would be killed if he stays [by the] same people who threatened to kill me if I didn't go along". With that information, Scully forced Mulder to leave, to stay hidden. The reasons of the grudge of the Supersoldiers against Mulder in particular will be revealed in 9X11: Providence. Kersh may be painfully by-the-book but he holds some regret that things are as they are: the Supersoldiers have power, and resisting their orders might prove deadly. So Kersh left Doggett the obituary pointing to Wormus's death in order to make Doggett aware of that. Doggett was leading an internal investigation on Kersh, complicated by the fact that the FBI surveillance tapes with Krycek's murder and the car chase (8X21: Existence) were 'taken': 'they' had incriminating evidence against Skinner (and what the hell happened to Krycek's body?!). Doggett decided to follow Kersh's advice and to focus on more important things for the time being: to survive. Doggett brings Reyes along with him in he X-Files and Scully goes to Quantico to teach medicine. This is the X-Files 2.0.
Nothing Important Happened Today II
Reyes: "What are you doing here?"
Frohike: "You sent us hacking on this investigation of yours only we had a small funding fiasco."
Langly: "They cut our internet service."
Reyes: "Don't tell me you breached FBI security just to log on!"
Doggett: "You tell me. You looking just to get me fired or get me killed?"
Kersh: "You ever hear of King George III?"
Doggett: "You answer my question!
Kersh: "He was king of England when America declared independence in 1776. King George III kept a diary. On July 4, 1776 he made an entry in it: 'Nothing important happened today.'"
Doggett: "What the hell does that got to do with me?"
Kersh: "Revolution started. Things that changed the world forever. And even kings can miss them if they're not paying attention."
Doggett: "Just so long as you know here to reach us... Mr. Follmer."