All the dead Monolith and Military outside and inside X16 intrigue me. They appear to have been fighting, and possibly all died, but Sacharov doesn't mention anything about it. Since there are no corpses there in Clear Sky (at least not on the outside), the fighting must have taken place sometime between Clear Sky and Shadow of Chernobyl (unless the Clear Sky level design is a retcon). Does that mean living Monolith were hiding inside the lab during Clear Sky?
The game makes it clear that all O-Soznanie experiments were black book projects and thus, government had no idea about them. This way, after Zona was created, government regularly sends military raids, smaller teams and single agents to gather information.
The first such raid is mentioned by Sidor: it happened right after Zona was created. Military wanted to get inside and just blast the place to smithereens with a nuke. O-Soznanie has control over blowouts and uses them as a protective measure, so the first raid was obliterated by a massive blowout. O-Soznanie also starts blowouts every time someone gets too close to the center, as it happens during every Strelok's raid (the start and end of Clear Sky, the end of SoC).
Military uses all opportunities to seize more information: this is why you meet soldiers on Agroprom, they drop on you after you leave X-18 and after you switch off X-10 they start another massive raid.
With X-16, the scientists are nearby, and being smarter than military, they actively hire experienced stalkers to do the job for them. Obviously, scientists and military both work for government, but in different branches. After you switch off the emitter in X-16, scientists instantly call a couple of helicopters to clear the area.
In Clear Sky you can see many stalkers being hired by Sakharov: he mentions hiring Strelok but he disappears, then he hires other guys, and finally, Scar. Scar stabilizes the emitter and goes on his merry way.
Now, O-Soznanie has no outside tools other than Monolith, and they had to protect relevant X-labs to prevent people from gathering too much information about them. This is especially relevant to X-16 lab as it has prototype emitter and can allow people to create PSI protection measures to go through Radar.
We may assume that O-Soznanine somehow learns about scientists making progress on Yantar (could be another Strelok mad dash and crowd of Clear Sky stalkers on Chernobyl at the end of Clear Sky) and decides to actively stop it, sending a major Monolith unit to seize Yantar and remove scientists/stalkers from there for good.
Stalkers are getting massacred, so this why we see lots of dead stalkers and zombies on the map in SoC but no one alive aside from scientists. Scientists call military for help and they start blasting each other with Monolith, hence lots of deaders from both factions around. Again, we can assume that military wins but has to retreat, being fried by X-16 emitter.
Another version is that after Scar stabilizes the emitter, military decides to use the opportunity and seize the facility. This prompts O-Soznanie to send Monolith unit to prevent it, and stalkers getting caught in crossfire. Hence lots of deaders.
Pick what you like more