Edward Wilson (Matt Damon) is a serious, quiet, and idealistic student at Yale who is recruited in 1939 to join the secret Skull and Bones society, an elitist group of powerful men who deem themselves as the saviors of democracy and the leaders of industry and government. Although he is dating a lovely deaf girl he meets at the library, at a party he has sex with Margaret "Clover" (Angelina Jolie), the sister of a wealthy and conservative friend from Skull and Bones. She becomes pregnant and he agrees to marry her. Their relationship, however, soon takes second place to his career.

Edward is sent to work for the Office of Strategic Services (OSS), the precursor to the CIA, during World War II. His right hand man in London is Ray Brocco (John Turturro). Following the war, Edward returns home to his unhappy wife and lonely six-year old son, Edward Jr. (Austin Williams). The two parents dance around each other but never are able to connect in any meaningful way. The son is frightened of his remote father and cringes in his presence.

Edward is handpicked by General Sullivan to direct the new CIA's counter-intelligence unit that uses disinformation as its main tool. He works under Philip Allen (William Hurt), the director. One of the first chances to prove himself comes with the secret Bay of Pigs Operation that involves an invasion of Castro's Cuba. But due to someone blowing the cover, the mission turns into a disastrous fiasco. Sam Murach (Alec Baldwin), the FBI agent who first approached him on campus to work with the government, tells him that he is being blamed for the mess. Edward's idealism turns into bureaucratic pragmatism as he becomes a hardened man with no pleasures or expression of feeling. He becomes obsessed with finding out who the traitor is.

Robert De Niro does a masterful job directing this espionage tale that works so well thanks to its talented cast. The intelligent screenplay by Eric Roth (Forest Gump) is the key to the film's clout and insights into the word of spying, counter-espionage, the rivalry between the United States and Russia, and the kind of rigid patriotism that leads to paranoia. Mostly it is about the many ways in which power corrodes the soul and how secrecy destroys any possibility of a true relationship. Several colleagues warn Edward not to trust anybody, either apparent friends or enemies. His son complains that he never felt safe as a child because "everything was a secret."

Matt Damon is just right as the humorless and driven CIA operative who is willing to sacrifice love for his family for his work. This comes across with irony in that the Russians' code name for him is "Mother." Edward is exposed to a variety of individuals over a three-decade period who test his moral mettle and compel him to clarify his values. They include his son Edward Jr. (Eddie Redmayne) who grows up and joins the CIA; Laura (Tammy Blanchard), his first love; Dr. Fredericks (Sir Michael Gambon), a professor at Yale who takes a personal interest in him and later provides some invaluable advice that is ignored; Richard Hayes (Lee Pace), a rival at Yale who is a fellow member of the Skull and Bones society and a man who doesn't appreciate Edward's personal style of secrecy; Arch Cummings (Billy Crudup), a friendly British spy; Valentin (John Sessions), a Russian defector, and, last but not least, Stas Siyanko or "Ulysses," (Oleg Stefan), Edward's counterpart in the KGB.