What is the main plot of the F.E.A.R(Pc Game) saga?

The soldiers are an army of clones that the government created. The idea is that they can be controlled telepathically by a single psychic commander. This guy Paxton is controlling the clones for his own purposes which were unintended by the government who made them. He's kind of gone on a crazy rampage with them. I don't know how far you are so I don't want to spoil the plot surrounding Alma. Let's just say she's pissed, wants revenge, and you'll find out why and what she has in mind later. Enjoy the game!