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As far as I can tell the colonization arc (up to the end of Season 6) proceeds thus:

  1. The colonists are an alien species that exists as a virus that has the ability to control hosts and to begin the genesis of a specific kind of host within the initial host. The gestating new host feeds off the body of the initial host. The newly generated host (a large clawed alien) eventually matures into a diminutive grey alien.
  2. The colonists visited Earth before the end of the last ice age. However they don't take well to cold, and so they left.
  3. The colonists first known return visit was in 1947 when they crashed at Roswell.
  4. President Truman learns of their plans and threatens to nuke the entire planet (and thus render it useless) if they invade.
  5. Consequently, the aliens (I presume) put aside their plans for an old-school guns-and-bombs invasion and decide, instead, to quickly infect humans with the virus that is the first phase of their life cycle (which accompanies every phase of their life cycle in the form of the black oil).
  6. In order to do that, the aliens need an inconspicuous viral vector. Presumably, just spraying the virus everywhere from some kind of craft would be a conspicuous attack and prompt the humans to use the nuclear scorched-earth option. They decide to genetically engineer bees to harvest the virus from crops (genetically engineered to include the virus within their pollen) and then infect humans with it.
  7. Farming and beekeeping, as well as the genetic alteration of the products thereof, require a presence on Earth (at least in order to be done efficiently). This would expose the colonists to the danger of discovery and, consequently, to losing the Earth to nuclear weapons. Perhaps for those reasons (or just because it's easier if you have The Man on your side), they contact the people who engineer events on Earth (the syndicate) and arrange for the syndicate to ensure the smooth execution of their plan in exchange for some alien genetic material and a bit of time (until 2012) to research that genetic material in order to attempt to develop a vaccine for the syndicate members and their loved ones before colonization. To make sure the syndicate makes good on their deal, the colonists take a member of the family of each member of the syndicate.
  8. Presumably, because the colonists don't want more more than the agreed-upon number of humans to escape the effects of the viral attack, the aliens send a bounty hunter to kill all the humans that had been experimentally-vaccinated (and hybridized in the process) by the syndicate.
  9. Some guys in Russia unethically, but successfully, develop a vaccine.
  10. Alien rebels incinerate the colonist's research subjects and (effectively) all of the syndicate. Thus delaying the plan for colonization.

It doesn't seem to me that Mulder had any effect on any of those events. Am I wrong, or is Mulder, and his work, just a way of presenting that story arc?

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    If you have spoilers, don't tell us that there are spoilers, just use a spoiler tag >! to hide them – Valorum Aug 28 '17 at 22:28
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    President Truman wanted to Nuke the Earth?? I must have missed that! – n00dles Sep 16 '17 at 3:46
  • @n00dles He used it as a deterrent to invasion. His preferences would have been ordered: no nuking & no invasion > nuking & invasion > no nuking & invasion. – Hal Sep 20 '17 at 14:05
  • Yeah, it makes more sense why they didn't just invade now. Do you know which episode that was in, so I can look out for it, if you don't know the name, "The one where..." should do. – n00dles Sep 20 '17 at 15:38
  • @n00dles It's in a deleted scene from the series finale, "The Truth". – Hal Sep 22 '17 at 15:03
7

No effect

In "My Struggle III" (Season 11, Episode 1), Mulder encounters a surviving member of the original Syndicate — like most Syndicate members, he is nameless, although the subtitles for the episode refer to him as "Mr. Y". Mr. Y's associate explains to Mulder that colonization never occurred because the

aliens became disinterested in reclaiming a "warming planet with dwindling resources".

Of course, we are as per usual at the mercy of whether the characters in question are revealing or obfuscating the truth. However, note the following facts that pick up from where your chronology leaves off:

  • Despite the destruction of the Syndicate in Season 6, plans for colonization remained intact: preparations for colonization were being administered directly by the aliens themselves, in the form of Super Soldiers (Season 8-9).

  • Mulder, having been found guilty by a military tribunal for the murder of Knowle Rohrer (a known Super Soldier), went on the run with Scully in 2002 ("The Truth", the Season 9 finale). It is made abundantly clear that the Super Soldiers will stop at nothing to track him down.

  • In 2008, having seemingly evaded the Super Soldiers for six years, Mulder reluctantly returns from exile to consult for the FBI on a murder case (as seen in I Want to Believe, the second film). In 2016 (Season 10), he returns to work full-time for the FBI. Four years have passed since the supposed date of colonization, which had been repeatedly emphasized would occur in 2012. Furthermore, there continues to be no evidence of Super Soldier activity (see also this question).

So, it seems that nothing Mulder did in Seasons 1 to 6 had any effect on colonization, as the Super Soldiers arose to replace the Syndicate and work towards colonization on the same "timetable". Over Seasons 8 and 9, Mulder was mostly out of commission and the Super Soldiers only grew in strength and influence, cementing control at the highest levels of law and government.

During his period as a fugitive and his subsequent return to the FBI, colonization had been shelved (at least the original plan for it) and the Super Soldiers have disappeared. None of this seems to have anything to do with Mulder: in hiding, he was completely inactive for obvious reasons, and prior to his return to the FBI in "My Struggle" (Season 10, Episode 1) he seems to have been completely disconnected from anyone or anything that had to do with the colonization conspiracy. Whatever caused the Super Soldiers to disappear or become less obvious about their actions seems to be orthogonal to Mulder.

Regardless of whether the assertions of Mr. Y's associate are truthful or not, we can only conclude that circumstances independent of Mulder's actions are responsible for shelving or delaying colonization.

Indeed, Mulder's actions have always been simply a vehicle for revealing slowly the intricacies of the conspiracy. As an audience, we always know what Mulder knows — and nothing more.

William

Perhaps the one thing that Mulder did that might have had a tangible effect is to father a child with Scully, as events at end of Season 8 suggest that the special circumstances of William's birth may have posed a threat to the aliens. (Scully was previously barren and it was asserted by Krycek that the birth was influenced by a "higher power" in protection of humanity.) The Super Soldiers seemed determined to stop the birth and, in Season 9, we see William display vastly abnormal abilities.

In Season 11, Epsiode 1 we are also told by both Scully and the

Smoking Man (who is somehow alive...)

that William is immune to any viruses or pathogens of alien origin.

However, it is not as if William's special nature was planned by Mulder, and as of the end of that episode it is no longer even clear that

Mulder is William's father

and so again we are forced to conclude that Mulder has not done anything obvious to affect to the final state of affairs.

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