On the betrayal bit, I think the whole political and factional landscape is already very murky, so I don't think the waters would be muddied any further by developing a relationship between the Stalkers and the Combine. The three major parties I see co-existing in the mod are the Combine, the Stalkers, and the general public (refugees, murderers, bandits, treasure hunters, traders, etc). A possible forth party could be the Lambda rebels (this version of them would be more Russian Army in nature), but I would say they play a minor role at best...or could be viewed as amateurish, futile, or a HEY GUYZ I HAZ A BLOG AGAIN. Catch an extended reading of earlier paragraphs at it. Link in sig.
@Joe: mechanics like that are all very nice, but they add to development time and are ultimately not that a big a deal for something very small. It's easier to just give the player that choice rather than making a song and dance of it. I'd love an inventory system all the same though.
Y'know, I kind of like the 'twisted partnership' idea, but it seems a little too close to the usual betrayal stuff. It'd also complicate the relationship between the player and Stalkers - possibly very interesting if pulled off well, but equally it could be very frustrating.
Here's an extract from the synopsis, which I might add is still being modified - I think up these ideas at random. Hence the new date of 1986 etc.
When your father goes missing at the age of three, you accept that he was a casualty of the collapse of the Soviet Union. Many years later after the Seven Hour War, when your uncle escapes to a rumoured 'safe haven', you decide to join him. The safe haven is Ozorski however, a city abandoned in 1986 shortly after Chernobyl. While similar, [redacted] and for years was kept extremely secure by the Soviet military and subsequent Russian military. [redacted], the town was sealed. Many years later Kiev refugees escaped to Ozorski, only to find a more certain death at the whims of a 'Field Zone' that distorted time, space and the mind.
The Combine hunted the majority of refugees down, and in doing so discovered the Field Zone. The telepathic abilities of the Combine Advisors allowed them to interact with the Field somewhat, [redacted].
While the Combine [redacted], you also seek your uncle for answers on your father while you still can – he is the only one who knows where your father went. You will have to work with the few Stalkers who survive. Their numbers are too small to be considered a threat to the Combine, and they do not willingly engage them.

Yeah, SCP joke. Some things are pretty big spoilers.distraction in the eyes of the Stalkers and the general public alike.
The relationship between the general public and the Combine could be viewed as not being much different from their relationship with Soviet rule: a classless society that works for the government (in this case, the Combine). In that respect, the player can blend in with the general public, but may be forced onto his guard when an average citizen thinks he can snitch on the player and collect a reward from the Overwatch.
The relationship between the Stalkers and the Combine would clearly be more complex, and this relationship would directly influence the relationship between the Stalkers and the general public. More on that later. The Stalkers likely see the Combine as simply another collection of customers. They have somehow gotten onto the Combine's good side (like Breen somehow did) and now the Combine provide for the Stalkers and in exchange they get access to the Zone's mysteries. EDIT: I sat here and thought about it for another 10 minutes and I understand that the second- and third-order effects of such a relationship can quickly spiral out of control...its just a matter of choosing the ones that stir the most pots at once. Then again, I'm not the writing major.
In the STALKER series and its origin stories, the STALKERS guide people into the Zone in search of those fancy baubles that grant such incredible powers, etc etc etc. So these people are already on a higher level of prestige and/or hatred than the average citizen. If they start tak@banter: It sounds like you need a built-in holstering mechanic so the player can easily broadcast his level of force to passers-by. I imagine that if the Combine see a non-Combine carrying a weapon (or 10) they will get very suspicious. Come to think of it, it sounds like you need an inventory system and strict regulations on the amount of equipment and weaponry the player can carry around.
Another thing I wonder about (on a storytelling level) is the actual population of the area. This is supposed to be a "second Pripyat" that was abandoned in the Zone for nearly 45 years (1972-2015, that's 43 years). Now, your mod page says the city was silent for 30 years...so I am hypothesizing that after 30 years of silence, strange things began to happen and a population came to exist in the city. If this is the case, I hope some exposition is delivered regarding those 15-odd years of non-Combine development.
And then the Combine invasion occurred. Now my own personal take on the invasion's effect on human migration is that people fled from less populated areas due to the portal storms and Xenian happenings, and then they were corralled into the cities by the Combine, leaving many tiny pockets of humans out in the wild. So I have to wonder if the mod's city was considered by the Combine to be a suitable metropolis for the local human populace. If so, then the information you shared here earlier makes sense. If not (that is, if the Combine have taken a special interest in certain Stalker-like oddities and see everything else as a useless husk), then my opinion is that the Combine would round up everybody they could and ship them off to "safer places" like nearby City 17 or Nova Prospekt (nearby in terms of being on the same continent).
And even if everybody does get shipped out, that doesn't mean that the Stalkers would be captured by the Combine, much less subjected to maliciousness. In fact, an even more frightening concept in my mind is that the Combine form a twisted kind of partnership with the Stalkers, who continue doing what they do best: guide people into the Zone.ing payment from the Combine for the same trips to the Zone, then perhaps the populace will feel alienated. Perhaps they will feel betrayed. But I do not think they will betray the Stalkers.
The Lambda rebels might see the Stalkers as a threat because they are helping the Combine. The Stalkers might see the Lambda rebels as a threat because they are distracting the Combine from paying up for tours of the Zone.
Of course, since you have the master document and plot points in your possession, you have far more to work with in terms of providing motives to these factions and their individuals, as well as coming up with gameplay-friendly situations that can portray the story without much literal exposition. A particular artifact could be sought that performed X ability, and it could be the key to endless purified water or it could be the key to endless green slime. Or maybe a headcrab has become enchanted by the Zone and now this legendary elusive headcrab is running amok with superpowers, requiring an intervention from the Stalkers. Perhaps the Combine want access to the Wish Granter, and the player could lure an Advisor into the Meat Grinder.