I have the Gray Spirit, Project Vulture, and Byzantium mission icons still showing (plus two haven defence) , even though I finished them days ago. The game doesn’t seem to be progressing to an endgame - even though I’m at 97 - 100% with all three factions.
Just a note: Your relation with faction is not a measure of game progression.
If you want to know how to access final missions:
So I seem to be about the Yuggothian Entity/City on a Hill. I have researched all available tech. Any way to spark it, or just wait?
Typically, a target on the earth map appears for the final mission. Like a super Pandoran base. But perhaps your research isn’t quite enough yet.
You need to unlock and research:
-Adv. Missile Tech
and completing City Upon a Hill
you receive a location for the Palace after researching Project Nemesis
Sometimes after completing your objectives, it will take some time before the faction completes theirs.
Yes, they have to build the Temple(Anu), the Fortress (NJ) or Lunar launch(Synedrion)