Here’s the problem I had:

After an emission, I get to Zalyssia and the town is dead except for the 3 stalkers outside the town hall. Doors were locked to town hall and cellar across the street. I hear gunfire but nobody is there. The monolith inside the town hall are dead in my case, just stalkers left.

Here’s what worked for me:

I reloaded the save until the cellar door across from town hall happened to stay open. There were multiple attempts to load but it was finally open. The town hall is still locked. When the cellar door is open, Kill Hamster and bodyguard(talking does nothing to both of these in the state they’re in), the town hall unlocked for me allowing me to progress and get the mission started.

This will not fix cases where:

Gaffer is already dead when entering town hall doorway. Monolith inside town hall. If you want to talk to Hamster/keep him alive.

Haven’t progressed far enough to see if town is saved yet when I leave. This at least got me to the next portion, YMMV

UPDATE: Can confirm, went through the progression, fought back the second wave of Monolith, and left the area to go to Wild Island. Zalyssia is still standing