Who was flying the alien spacecraft in the end?

We were never shown.

"Are you sure it wasn't a girly scream?" - D.S.

It lets you to suppose that one of the aliens, after all it was the ship they came in

Never Hate Your Enemies, It Affects Your Judgement

I figured it was an automatic escape system. When trouble was detected, like Mulder injecting the cure, it was triggered to get the ship out of there and back home.

Do you remember the aliens gestating at the end chasing the main protagonist? There must be many aliens in the spacecraft.

Hasn't the syndicate been working with the aliens for years?

I don't think there is any reason not to think that there were aliens from a well established group; part of an over-seeing group, on site.

Uhh... Any one of the hundreds of aliens that began popping out of the human hosts as Dana and Mulder were escaping the ship?

Prof. Farnsworth: Oh. A lesson in not changing history from Mr. I'm-My-Own-Grandpa!

The craft was being maintained by human Syndicate workers. The gestating aliens were not working in tandem with them, that we know of, since they all appeared to be in a state of hibernation/development. When the craft left Earth it was most likely on autopilot, probably as a result of the quarantine breach caused when Mulder broke Scully out of her containment tube. I assume that there were only a few people other than Mulder, Scully and CSM who actually escaped. The others were either killed or whisked away by the craft to wherever.

-Rod

Martin Landau.