A series of alien/human clone hybrids, used as labour force by the Syndicate, tries to start its own program of colonization in hopes of surviving. A shapeshifting Alien Bounty Hunter comes on Earth to exterminate them; the cover story is that the hybrids are soviet clone spies. The clones, some of which are Samantha clones, ask for Mulder's help. After the ABH kills them all, Mulder follows him to a submarine in Alaska, where the ABH reaches his craft.
A colony of hybrid clones
What we encounter here are cloned alien/human hybrids, not alien colonists. Even if we speak of a colony begun by these clones, the clones themselves are simple flawed hybrids who know that when the real colonization comes, they will be killed off as useless waste products. In the meanwhile they're used to conduct more hybridization and cloning experiments, simple executives that are supposed to follow orders. The mere fact that among them are clones of Samantha Mulder connects them with the Syndicate; these can't be rebels nor other aliens as the Samantha clone's story suggests. In fact, the 'Gregor' and the Samantha cloned hybrids are placed in women's health care clinics ("all worked in abortion clinics") to have easy access to medical equipment and human tissue for their cloning experiments (Samantha: "Access to fetal tissue"). But knowing their ultimate fate they choose to rebel and start a colonization of their own. They're not the alien colonists, but they're not human either: their move to multiply and live out their lives freely as any ethnic minority can be considered as a colonization.
How to make your hybrid clone
Though we are fed with lies many times over in these episodes, these are cloned hybrids. Among lies, the Samantha clone says: "Through hybridization [...] though the biologies are incompatible, they finally found a way to combine human DNA with alien DNA". The Samantha clones do come from the original Samantha (how else would they know so much on the Mulders?), the male 'Gregor' clones must come from an abductee in the same fashion (see 6X12: One Son for some confirmation). The method is as follows:
The person that the Samantha clones were trying to save, the same person the ABH was trying to find ("Where is she/he?"), is the first-generation hybrid from which all the other clones were made. From there, theoretically, one could go on cloning the cloned Samanthas to create another n-generation hybrid, but this doesn't seem possible: "The rest of us are dispensable. She was the first. The one from which we all came. The one you must save." The first-generation Samantha is what's important, the one the ABH wants to exterminate, because she's the only one that can be cloned. Perhaps cloning second-generation hybrids has unwanted effects, like degrading the genetic material in the cloning process; it's like making a copy of a copy.
Alien & hybrid physiology
Scully autopsies Agt Weiss and finds he dies from blood coagulation caused by a "retrovirus", which seems to be what the 'green blood' is made of, not unlike the virus-carrying bacteria of Purity Control. Anything that touches to hybridization of Black Oil and human seems to be made of this green virus-carrying substance. Scully & Dr. Gardner determine that "the virus is inhibited by cold", it "goes dormant at cold temperatures". That's why Samantha's body is still preserved when it's recovered from the cold river, and starts decomposing when left in the warm air. Scully is able to save Mulder by making "transfusions and an aggressive treatment with anti-viral agents", which eliminate the retrovirus from his body, while keeping his body on a low temperature to inhibit the action of this retrovirus.
Mulder had a violent reaction to Dr. Secare's blood in The Erlenmeyer Flask but he didn't die. An explanation for this is that the 'blood' of the hybrids we meet here is 'purer', closer to the successful hybrid's 'blood', thus more toxic and lethal. Dr. Secare's 'blood' was toxic enough to cause a reaction but not enough for it to kill upon exposure.
When they die, 'green-blooded' aliens or hybrids turn into a gas-emitting green goo that's toxic and corrosive, and then vaporise completely (as the 'Gregor' Dr. Dickens's body under the fire escape).
The Alien Bounty Hunter
The ABH was called by the Syndicate to take care of this incident because the Black Oil aliens are the only ones who possess the stiletto, this alien toothpick which is, according to the Samanthas, the only means to kill hybrids of this sort. The ABH is new, the Samantha clone had never seen him before ("He's got powers I've never seen before"), he comes to Earth on his ship which crashes in the Alaska sea. All bearers of the 'green blood' have a sensible spot in the "base of the neck" ("piercing the base of his skull") but only a stiletto wound will kill these hybrids. Dr. Secare (1X23: The Erlenmeyer Flask) only needed a gunshot wound in the base of the neck to kill him. Therefore, the Samanthas and 'Gregors' are a new and better kind of hybrid, and the Syndicate need the Black Oil aliens' help to police them.
Is a stiletto necessary to kill an ABH? No definitive answer can be found here, there are arguments for and against. The Samantha clone wouldn't have risked her life in the Old Memorial Bridge exchange if a stiletto was necessary: she has Mulder put a sniper to kill the ABH. She tries to stab the ABH herself only because the gunshot isn't coming (a pillar obstructed the sniper's view); and when the sniper fires, one can barely tell if it was the base of the neck which was shot. In all cases, the ABH survived. He was also able to survive Mulder's gunshots in the submarine, but these weren't that well aimed either. So a stiletto could be necessary for an ABH too. As the Samantha clone says, she doesn't know the ABH so well, so she could have just wrongly supposed that he could have been killed with a simple gunshot, like with Dr. Secare. Confirmation will come in 6X11: Two Fathers.
The ABH is capable of shapeshifting, but the cloned hybrids don't have this ability (or any clone could have made Mulder believe he was Samantha). However, both ABH and hybrids are able to communicate through telepathy (the hybrids can tell the ABH even if he's taken another form).
We never meet CIA Agent Ambrose Chapel, we only see the ABH impersonating him. Perhaps Chapel doesn't even exist, perhaps he's an identity created by the Syndicate specifically to ease the ABH's infiltration in this US organization and for him to use all the access and investigative equipment the CIA provides. The story the ABH presents to M&S, that the clones are Soviet 'Gregor' spies, is a story coherent enough and believable enough to make M&S go away, especially since it comes from the mouth of a CIA agent. The ABH crashes in the Beaufort Sea, between Alaska and Russia, and is described in the media as "a Russian fighter pilot"; the crash was arranged so as to fit the 'Gregor' cover story.
Samantha's (fake) story too in some way reflects the cover story: "The men you've been seeking are the progeny of two original visitors, clones who have been attempting to establish a colony here since the late 1940's", basically the same story only substituting soviet spies with aliens. This version of the truth points to Roswell and a group of identical-looking aliens trying to colonize since then; the clones and the ABH would then be real aliens of the same kind. The ABH would be sent to kill the clones probably because of the fact that they mixed their genetic material with the lower humans, this alien race being obsessive with genetic purity (cf. 'Purity Control'). This story would also make the 'Gregors' and the Samanthas clones of the "two roginal visitors": the Samanthas would be no clones of Samantha Mulder at all, but clones of the alien colonist. To make things even more complicated in the tortured process of stroywriting in the X-Files, this story would be the true and final version of the truth at the time it was written (as the whole story arc culminating in 6X12: One Son was still in its inception phase). A bit of tweaking as explained above is necessary to reconcile the 'truth as of 1996' and the 'truth as of 1999', as always in XF...
We meet the Mulders. Bill & Teena are divorced (Mulder's surprised to find his father at his mom's); the divorce probably happened right after Samantha disappeared, Fox most likely stayed with his mother afterwards. Teena is very shocked to see Samantha return, but Bill is cool, most likely aware already that this is nothing but a clone. We're not aware of Bill Mulder's part in the Syndicate yet (2X25: Anasazi) but his distant stance and harsh words to his son are in accord to his long-term plan to harden Fox's feelings in order to feed his will for exposure of the Syndicate's deeds (Fight the Future).
Another thread is begun here: when Mulder asks "where is she?", the ABH finally answers that "she's alive". Of course in Carter's mind Samatha was still alive at that time, the twist of 7X11: Closure is still far away, but the ABH's words can be explained. The ABH works here for the Syndicate, and it is the Syndicate's policy to manipulate Mulder into a blind crusader that can be easily fed with lies that discredit UFO lore and ease the Syndicate's doings at the same time (5X02: Redux). To tell Mulder that Samantha's still alive fuels Mulder's quest in the best way possible ("faith to keep looking"). Whether she is or not is irrelevant. Or, the ABH just wanted to get rid of Mulder. Even the Samanthas manipulate Mulder ("We knew you could be manipulated"), using their physical appearance to enlist his help. "We know where your sister is. Ask yourself, Agent Mulder, how else would we know so much about her?" It is true that the clones know much of Samantha Mulder's history because of their ascendance, but this line is another manipulative attempt to give Mulder another reason to save the clones from the ABH.
Scully knows of Mulder's trick with the taped 'X' and blue light, but X is willing to give information only to Mulder himself. Skinner has to 'beat' it out of him. Skinner probably knows X already, having seen him with the CSM (X works for the CSM -- 3X23: Wetwired). It's become a kind of trademark of X to participate in violate scenes, and it will become worse later; nothing to do with the paternal figure of Deep Throat.
Again, the only ones who move against the aliens (here, the ABH) are the military, not the Syndicate itself (not even CSM appears here). The submarine USS Allegiance tries to destroy the underwater UFO just before the power loss, and X tells Mulder that "an attack fleet left port from Anchorage" to obstruct the ABH's return. The Syndicate and the aliens must have an understanding that if a UFO goes down, the Syndicate won't obstruct the army from destroying it. The ABH's craft was able to immobilize the submarine and the ABH killed its crew to make sure he'd have a safe passage to his craft. In the end, the ABH goes back to Alaska and uses the US army submarine to reach his craft; but he doesn't leave Earth (we see him again in 3X24: Talitha Cumi).
After this episode, there is little doubt left that there's something 'weird' going on. As Mulder says, "I will have already learned the answer [...] there is intelligent life in the universe other than our own". A shapeshifting 'man' with superhuman strength, clones that bleed green, an unidentified toxin... Scully has seen all this yet after this we will still see her as skeptic as before, time and time again. It's the point where the viewer's suspenion of disbelief takes a blow. Scully and Mulder are two almost caricaturised characters that stand for ideas, skepticism and belief. That's why Scully keeps refusing to believe, or it would be too easy. The tricky thing is to write stories where both explanations, scientific and paranormal, are equally plausible. As the series progresses, this becomes increasignly difficult.
Mulder's teaser monologue: "I have lived with a fragile faith built on the ether of vague memories from an experience that I can neither prove nor explain. When I was twelve my sister was taken from me. Taken from our home by a force that I came to believe was extraterrestrial. This belief sustained me, fueling a quest for truths that were as elusive as the memory itself. To believe as passionately as I did was not without sacrifice, but I always accepted the risks. To my career, my reputation, my relationships... to life itself. [...] What happened to me out on the ice has justified every belief. If I should die now, it would be with the certainty that my faith has been righteous. And if through death larger mysteries are revealed, I will have already learned the answer to the question that has driven me here. That there is intelligent life in the universe other than our own. That they are here among us. And that they have begun to colonize."End Game
Mulder: "That's a good story... but I've heard a lot of good stories lately."
Samantha: "I've got no reason to lie to you. I'm your sister, Fox, you have to trust me."
"Where is she?" (ABH on the hybrids, and Mulder on the original Samantha)
Scully: "Did you find what you were looking for?"
Mulder: "No. No. But I... I found something I thought I'd lost. Faith to keep looking."