The aliens' plan of releasing a sentient virus to, in effect, terraform human bodies into human/alien hybrids whom would have their consciousness downloaded... it got *seriously* disrupted when Mulder injected the antidote into the main colonization ship, at least a decade or two too early.
Now, they would have to traverse the stars, and we have NO idea AT ALL if FTL travel is even possible in the X-Files universe (all of the alien vessels could have been coming from the Antarctic mothership), so maybe it will take them 20 years to get here? maybe 2,000? Maybe they have parked motherships in reserve 30 years away from Earth? who knows?