The plot of Alpha Protocol is more twisted than pretzels baked by M.C. Escher. It's one of those stories where nobody is who they seem to be, and every organization is hidden behind a front, which is covered with a facade, which is concealed by a conspiracy, which is actually hidden behind something you'll have to look up in a wiki if you want to make any kind of sense of it.
This is as is should be. A straightforward spy story is like a Star Wars movie without the lightsabers and Twi'lek side-boob. The confusion is part of the charm. Still: I'm going to need to play through this game again to figure out who I've been shooting. I may even need a third play-though to find out why.
This is definitely a game you want to binge on. Playing in little one and two hour chunks is like watching L.A. Confidential for ten minutes a night. It will run the plot through a mulcher and the resulting pieces will be too small to assemble into anything coherent.