You should deffo look up Stalkers A-Life system, and especially mods that restored many of the A-Life features that were dummied out of the production release's code. A-Life had a lot of stuff going on with NPC stalkers taking on quests, animals moving from region to region. I think they turned it off because it made the game unpredictable to the players in ways that weren't fun. Things like you get to an outpost and everyone's dead because mutants killed them when the player was somewhere else, but from the player's perspective a bunch of NPCs died for no reason.
Cepheus protocol has something like this. The player is part of a government agency that has to fight zombies in order to find a cure and stop patient zero. The player controls squads of soldiers and scientsts, builds fortifications, builds refugee camps to manage civilian evacuations, captures points in the city to get resources.
The zombies have an AI RTS engine going. They start out in one part of the city and over time they send infection units to increase the infection level in a given city district. Civilians are actually a re-source that the player and the zombie AI are fighting over - The zombie AI tries to take over districts of the city and as it converts more civilians it's able to send more zombies at the player as well as infect other parts of the city. The player, meanwhile, wants to evacuate civilians from the city to deny the zombie AI more territory and more zombies. Managing civilian evacuation is one of the game's most unique aspects. The player can build refugee camps, screen incoming civilians for zombie infection, shoot anyone who is infected, and evacuate survivors out of the city. You're dealing with tens of thousands of civilians so it's a significant infrastructure task and civilians on the move are vulnerable to attack. It's usually in the players interest to build large numbers of shelters safely behind protected walls so the player can screen civilians and put them in a safe fortress where there's little risk of them turning in to zombies under the AI's control. You want to get all those people on helicopters ASAP. You can also massacre civilians as an evil way to stop them from being infected which will make some AI factions turn against you. I think your own soldiers have some kind of morale mechanic, too, that makes massacres an extreme option instead of just a lol evil gamer thing.
In my campaign I ended up in a losing numbers battle against the zombie RTS AI. Due to lack of experience and some iffy game mechanics I was only able to evacuate and control small parts of hte city while the infection had completely overtake significant areas. I bombed the bridges between islands where the infection was strongest but I was still getting gradually over-run by increasingly evolved zombie enemies. It got to the point where I was only holding one district because I had a gauntlet of tanks and machine guns that could fire down one long, narrow street with high walls on either side that the zombies had to move through. Once they found a way to flank me I was forced to evacuate the whole district. The math was simple; The infection was overwhelming me and infecting civillians far faster than I could stop or contain it. In the end I had to load all my soldiers on to the aircraft carrier that acts as your home base then use LCAC hovercraft to launch a beach assault on the zombies primary stronghold. I abandoned the city to make a last-gasp decapitation strike against the super-powered Patient Zero AI because there was no way I could win a drag out boxing match.
All in all it was very cool with game systems interacting to create an emergent narrative. From what I understand the game has enough depth and variables that different campaigns can play out in wildly different ways based on the game's starting conditions and the player's tactics, skills, and knowledge.
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