where can I find alien bases?

[ZaWarudoWRYYY]

Just deal with BlackSide, no other alien facilities on map but avatar project still running and its fast, halp!

[Arcalane]

Look for missions that offer 'Intel Package' as a reward- the Package can be a Facility Lead that you need to find the other sites.

Also, pay attention to the progress messages. They may occasionally (accidentally?) announce where the progress is coming from, giving you an idea of which regions you need to be making contact with. As with vanilla, you can't attack a site until you've made contact with the region it's in.

[ShockmasterFred]

I would go to an alien bar and get an alien drunk. They can't hold their liquor and spill their guts after a few drinks, and hey, if your lucky, you might get lucky. Just don't play them in pool. Those aliens are all hustlers.