As far as I can tell the colonization arc (up to the end of Season 6) proceeds thus:
- 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.
- The colonists visited Earth before the end of the last ice age. However they don't take well to cold, and so they left.
- The colonists first known return visit was in 1947 when they crashed at Roswell.
- President Truman learns of their plans and threatens to nuke the entire planet (and thus render it useless) if they invade.
- 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).
- 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.
- 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.
- 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.
- Some guys in Russia unethically, but successfully, develop a vaccine.
- 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?