Well, the vanilla outcome is "The council gives up on a common defense, each nation tries to negociate with the all-powerful alien". If I had to imagine an alternate (playable) hypothesis for a "UFO : Resistance" scenario :
- Intense UFO activity while the alien openly spread their control.
- There's no way the entire XCOM personal accepts to go rogue, so you can expect most of your scientists, engineers and soldiers to go back home.
- XCOM is actually outlawed, because there's no way the funding countries can negociate if they cooperate with an alien-hostile faction. You can expect countries to give up XCOM bases position, if not move the entire regular army on them.
- Buying and recruiting become extremely problematic, because people take a lot of risks trading with the former XCOM. Don't expect "infinite" supply.
- Selling seems outright impossible, because who is going to buy alien weapons, which would get them executed if somebody knew they have it ? The only possible income must be from criminal activity.