Hello.
Does the mod have a victory condition?
I completed the mission of destroying the protomolecule nest, but I found 2 more nests nearby, and a little later a message about more nests appeared. Moreover, they appear outside the explored area and are not shown in missions. It is VERY difficult to destroy them, there are huge crowds of opponents, they are much stronger than me.

Not yet. So no more active missions right? I'd like to know how you dealed with them. In private to avoid spoilers. Also I need to think on the next steps, a way to eliminate them for good. Maybe a special mission to create a biological weapon or something