There are two main factions and a smaller third faction, within the world of Far Cry 3: Blood Dragon. These are the two main factions, the Omega Force and Scientists, as well as a third smaller faction, that being the Running Dead.
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Scientists[]
The Scientists are allied with Rex, the protagonist of the story. They wear white lab coats and in the open-world travel in packs of 2-4. They can often be seen fighting members of the Omega Force. They do not appear to have ranks or classes of any sort.
Omega Force[]
Omega Force is the faction that represents that vast majority of all enemies you encounter and fight throughout the story. They are spit into nearly a dozen individual classes, all of which have their own weapons and behaviors.
Running Dead[]
The Running Dead are mutated forms members of the Omega Force, making up 3 subclasses. While technically allied with the Omega Force, they will attack any faction on sight.