The film chronicles the foundation of the CIA through the life of Edward Wilson (Damon), a fictional spy who participated in its predecessor's activities. Over the course of the film Wilson's dedication to his work is contrasted with his detachment from daily life as he fails at being both a husband and a father.
This film provides examples of:
- Bodyguard Betrayal: Wilson, essentially the head of the nascent CIA, occasionally meets his Soviet counterpart, codenamed Ulysses. Late in the film, it's revealed that Ulysses' aide is funneling information to the Americans, direct from the source. The aide doesn't kill Ulysses or even cause him any direct harm, but his actions are definitely a betrayal in the general sense.
- Book Safe: One can apparently also conceal documents between the inside of a book cover and its lining without removing any pages at all.
- Chekhov's Gun: The copy of Ulysses. Yuri Modin's passport in hidden within the cover.
- Churchgoing Villain: Edward Wilson is an Anti-Hero version of this. He is a practicing Christian who has verses from The Bible inscribed on the walls of the CIA. He is also willing to drug, torture, and kill people. He's also a Noble Bigot with a Badge.
- Defector from Commie Land: Valentin Mironov is a former KGB agent who defects to the United States to assist Edward Wilson's counterintelligence unit in the new CIA against the Soviets.
- Excrement Statement: In the pre-war segments, there's a Skull and Bones initiation that involved members urinating and defecating on the initiates from an indoor balcony.
- Fake Defector: A long-term example, where a Soviet defector named Valentin Mironov spends years working with Edward Wilson in Wilson's counterintelligence unit. Another Soviet defector later shows up to claim that he's the real Mironov, while the first one is actually Yuri Modin, a KGB agent. They don't believe the second "Mironov" and torture him until he jumps out a window to his death (it doesn't help that he's dosed with LSD at that point). The first "Mironov" offers to take a polygraph test to prove that he is who he says he is, but Wilson refuses. Later, though, Wilson shows up on Mironov's doorstep in the middle of the night and demands that Mironov play his accordion. When Mironov agrees and asks why, Wilson replies that he wanted to finally hear something from "Mironov" that was true. Obviously, he figured out that the second "Mironov" was the real deal.
- Honey Trap: Used repeatedly by nearly every woman in the entire movie!
- Long Song, Short Scene: There is an arrangement of "Oh Shenandoah". Of course, we only hear part of it, and in the background behind the dialogue. It is MIA on the soundtrack, and hours of aggressive searching on the internet have turned up fruitless.
- Never Trust a Trailer: They pinned the movie as a deep look into the history of the U.S. Central Intelligence Agency, better known as the CIA, including scenes of supposed espionage underway. Really much of the movie is about the personal life of Edward Wilsons various affairs with women and his struggling marriage. And he just happened to find a secretive agency that spends most of its time trying to decipher a mysterious video. The movie is well over two hours long!
- No Historical Figures Were Harmed: Edward is basically a fictional re-imagining of James Jesus Angleton. Similarly, Archie Cumming is based on Kim Philby.
- Not the Fall That Kills You: Averted with Edward Jr's fiancée Miriam, who is thrown out of a plane in mid-flight and doesn't survive.
- Obfuscating Disability: A woman is pretending to be deaf since she needed some way to use a recording device without being obvious, so she masks it as a hearing aid. She gets found out when the main character calls to her from behind, and she reacts.
- Sarcastic Title: Edward Wilson, an emotionless robot of a man who built up the CIA, can hardly be called a good shepherd. Even in his private life he ultimately does more harm than good.
- Shotgun Wedding: Edward gets Clover pregnant the first time they have sex, which is also the night of the day they meet. Her brother tells him "I know you will do as expected". He does, despite being in love with another woman. He then leaves a week after the wedding for six years to fight in World War II and after returning, becomes a workaholic in the newly established CIA, rarely seeing her. The marriage ends in divorce.
- Spy Fiction: Stale Beer-style.
- The Stoic: Edward Wilson is almost emotionally dead. This was possibly the result of witnessing his father's suicide, but as an adult he's closed off to his wife (whom he doesn't love anyway) and his son, barely has a reaction when his mentor is killed, and even sends his son's pregnant fiance to her death with no remorse.
- Truth Serum: Subverted in a disturbing, graphically realistic way. Edward Wilson, the head of the newly-formed CIA's counter-espionage branch, is confronted with a Soviet "defector" who may or may not be who he claims to be. In order to determine the man's real identity, Wilson has his men administer a brutal physical beating. When they still aren't sure, they use a newly-developed truth serum called "Lysergic Acid" (better known as LSD). Rather than the above-mentioned effects of "Hollywood" truth serums, the LSD does what you would expect from reality- the man babbles like an idiot and hallucinates. Later, when the drug begins to wear off somewhat, he delivers a "Reason You Suck" Speech to his interrogators... then jumps out the window to his death. In case you were wondering, he really was who he claimed to be, making the tragedy all for nothing, and highlighting the ineffectiveness of the so-called "truth serum". This was based on a real incident where a man who was given LSD without knowing threw himself out of a window while hallucinating. He wasn't a Soviet defector, though, but a CIA agent given the drug by his own agency to test its effect on unsuspecting subjects.