GM fiat modify this thing
http://www.d20pfsrd.com/bestiary/monster-listings/aberrations/akata
There's a kind of worm-thing in Beastiary 5 that can do this, though only to spellcasters.
There is also the Incullus, though those kill immediately then control the corpse like a puppet. These are noticable as the Incullus becomes a mollusk hat on the corpse.
Also the Intellect Devourer, which is similar, as it it kills and takes the corpse, but this one will still seem like a normal being for a little while, as the ID plays puppet master from inside the hollowed out skull.
The Cythnigot Qlippoth will slowly grow and take over a host, turning it into not just a zombie, but a horrible deformed mutant zombie, but ti tends to stick to small animals.
The Yellow Musk Creeper is a plant that can infect people, first entrancing them with pollen then boring tentrils into their brain. After a few rounds of Int damage, the creature dies and becomes a Yellow Musk Zombie.
And probably many more!
Contributor
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What you need is the umbral shepherd, from the Inner Sea Bestiary.
It might not be exactly what you're looking for - CR 5*, incorporeal - but give it a look. ^_^
*The degenerate creature template (from Bestiary 5) might help you here.
that can get into a being and slowly takes over their body and controls them like some sort of flesh puppet? starting out like a necrotic plague. i don't wana just throw zombies at the PCs they are not so scary any more. but something that worms inside and slowly kills you while controlling your body while you watch and can't do anything has potential. sure the players will still tear through them like a hot knife through warm butter. will they players kill all of the infected and damn themselves or will they risk trying to save the newly infected and risk damning everyone else? that is just a little of something i wana bring to my players. so is there a necrotic flesh golem plague thing i don't know about in pathfinder?
There is a mechanic, I am unsure if its pathfinder or not, but it basically revolves around the "taint" mechanic in which different creatures, places contain taint. accumalating such taint has small negative affects, and by the end of the adventure path they are almost swimming in it.
So you could try looking that up, creatures could inflict wounds, and the PC's can slowly gain "taint" and it can slowly change how their characters react and feel.
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Mindslaver mold - though it might be too easy to rescue someone from that.
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Polymorphic Symbiotic Worms. They replace and eat failing organs and tissues causing a kind of immortality. As soon as the brain fails they turn chaotic evil. They are a swarm and thus parts already replaced are immune to most weapons. In a case of a plague, almost everybody will go along with becoming hosts.
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In one of the 3.5 Monster Manuals there were the Mockery Drones.
They're more like body snatchers in the way they take over hosts, but they make for beautiful horror adventures. They live in a hollow imitation of the basic habits of their hosts (a villager might carry empty pails from a long since dried up well all day, a town crier repeats the same message all dayetc.) and when they're found out, they burst from the host body's face, revealing their centipede like form, still with the hosts own face and the headless host body is left behind.