Basiclly the movie is a loose interpretation of the story of James J. Angleton as the director of counter intelligence for the CIA. He was a skull and Bones member-as well as a Knight of Malta(thats not in the movie)
Edward Wilson is the name they give him in the flick but theyv'e admitted to the changing the names-Like DeNiro plays as Bill Sullivan in reality it was Bill Donovan.
It flashes back and forth from the beginning of his entrance with the S&B up until after the Bay of Pigs thing which is where the movie starts.-Wikipedia does a good job of breaking it down, but the story is very hollywood as far as diverting from the truth even though its based on actual events but the story for the most part was accurate. They just hint at the cold war hoax but you can see that the CIA and the KGB practically worked together...