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NOTE: This spoiler sent in by BG.

The movie begins in 1961. Edward Wilson (Matt Damon) is building a ship in a bottle. He gets on a bus to go to work and a young boy asks if he has change for his dollar. He does. We then see him in the office using the serial number from the dollar to decipher a message.

It shows a brief montage of the Bay of Pigs and the CIA's failure to oust Castro. After viewing the dead bodies on the beach, Edward tells Brocco (John Turturro) there is a stranger in the house. They know it was an insider who informed Castro (or more likely Moscow). Later, a photograph and a recording on reel to reel tape are dropped off anonymously to Edward. His cannot identify anyone in the photograph as it is grainy and there's too much noise on the tape to distinguish anything. He gives it to his department to find any clues.

Edward goes to a diner and meets with an FBI man (Alec Baldwin) who leaves and forgets his hat. Edward is about to tell him he forgot his hat but then feels under the brim. He finds a cleaning ticket. He goes to a dry cleaner and gets a package. It has a shirt and under the shirt is a dossier on Phillip Allen (William Hurt).

This film is not told linear, but jumps back and forth from past to the films present which involves mostly the investigation of the mole. To keep it clear, I will tell each story separately.

Flashback to 1939. Edward is going to Yale and asked to join the Skull & Bones Society. He does knowing it is a brotherhood with powerful connections. It is there he is told to reveal something no one knows. He talks about his father's suicide as a young boy, how he found the note and hid it from his family. When asked what it said, he says he never read it. He is approached by a professor (and hit on) to join his group. Also while studying in the library, he meets Laura, a deaf student. He then is approached by a FBI (Baldwin) to spy on his poetry professor who they believe has Nazi connections. He does and exposes him as a fraud. His professor resigns.

In their first romantic tryst, Laura shys off and nothing happens. As he walks her to her door, she thanks him for being a nice guy. At this time, he has her crucifix in his pocket and decides to keep it.

Edward then attends a Skull & Bones Society meeting on Deer Island in 1941. It is here me meets Clover, a sister of a classmate and fellow Skull & Bones member as well as a Senator's daughter. Before dinner, a question is asked (which I can't remember exactly) like "Skull & Bones" and all the members stand up and say, "Present." They then will say a prayer to which Clover remarks to Edward Brotherhood before God.

It is also here that he meets Sullivan (Robert DeNiro). He asks him to join the OSS and lets him know fellow S & B members are part of the team. He wants him to go to London. Edward accepts.

Clover and Edward have sex in a secluded part of the island.

Edward is then on the beach with Laura. Clover's brother informs Edward that his sister is pregnant and should do the right thing. Edward is too late to block Laura from reading lips and she knows the bad news.

Edward marries Clover and is almost immediately sent off to England where he spends the next 6 years in the war effort. He meets with a British intelligence Officer (Billy Crudup) and Hayes (Lee Pace), a fellow S & B and classmate. He is then to be tutored in espionage by a seasoned pro, his old poetry professor. Edward apparently ruined 2 years of undercover work and he was trying to infiltrate the Nazi's for British intelligence.

It is here when he recruits Brocco to be his assistant. As the war comes to a close, he then must also take part in the killing of his poetry professor as he as become indiscreet and knows too much.

Edward also recruits a translator who wears a hearing aid. She has been aiding in documenting the scientists and other important German nationals who may prove beneficial to the U.S.

He is then asked to meet a Russian liaison who has been doing the same for the communists. Edward was warned that Russia would take as much land as they could. The Russian man is known as Ulysses. He informs Edward that he is known as Mother. They trade lists. Ulysses makes a comment about his hand being frostbitten. He says the cold is his weakness. He also comments how Edward is very silent. Ulysses tells Edward they will become mortal enemies and friends. Edward basically remains mostly silent. When Ulysses leaves, Edward tells Brocco that there's a stranger in the house.

Edward then has an affair with his translator. He figures out she is the mole and then she is killed.

Edward returns home. He meets his son, Edward, Jr. for the first time. He gives him a ship he made and put in what looks like a glass watch casing. His wife informs him she is no longer Clover but called Margaret. And she asks him to sleep in different beds until they get to know one another again. He is approached again by Sullivan to help form a foreign intelligence organization and wants Edward to work with Hayes and under Allen.

As life continues, his son grows up and learns how to make ships in a bottle and his marriage is a little sour. When his wife has friends over for dinner, they ask if he really works for the CIA. Edward replies that his wife has an overactive imagination and that he is just a civil servant. They fight about this later. She then questions what kind of life they have. He then tells her it was because she was pregnant was the only reason they got married and that it was the right thing to do.

Edward then is given an assignment to interviewing a Russian wanting asylum and claiming to be a high ranking official who knows Ulysses. He knows Edward as mother and that Ulysses' weakness is cold. The defector is named Valentin. He has all the correct papers. He claims to know other U.S. operatives in Moscow as well as Russian operatives around the world. He is interviewed and teamed with Edward.

Edward attends a production (of a Russian play) The Cherry Orchid with Valentin who claims it is a bad translation. It is at the theater that Edward runs into Laura, his college sweetheart. He has a passionate affair with her.

At a S & B party on Deer Island, Edward goes to the ding hall while Margaret gets dressed. Ed, Jr. has become a young man and is following in his fathers footsteps. He will attend Yale and join the S & B Society. While alone in the cabin, Margaret notices an envelope on the floor. It contains photographs of Edward and Laura. She causes a scene, interrupting a show with Allen and others on stage, and they both leave the dining hall. He then has a quick discussion with Hayes regarding the Bay of Pigs. His son overhears it. Edward tells his son he cannot repeat what he overheard to anyone.

Back in D.C., Laura is waiting for Edward at a theater, but Brocco shows up, gives her the crucifix and leaves.

At this time, another Russian who claims to be the real Valentin shows up. He tells officials that the man claiming to be Valentin is really Ulysses' right hand man. Valentin is present and watching the interview. They beat and torture the man who story never deviates. They then give him a dose of LSD, an experimental drug that might work like a truth serum. He starts to get high. He then tells them he is the real Valentin and then jumps out the window, killing himself. Valentin then tells Edward he will take the LSD. Edward tells him it is not necessary.

Edward visits Ed, Jr. at Yale. Ed, Jr. tells his father he has been approached by the agency looking for young recruits and he wants to sign up. Edward tells his son it's a difficult life. He tries to talk him out of it. Ed, Jr. is adamant.

Now we are hitting the time of the investigation. After analyzing the photograph (like forensics) they claim the man is Caucasian and the woman African. They can figure out there are three steeples, the make of the fan as well as the type décor on the walls & the furniture, and the time of day from a clock on the night stand. They cannot identify some blurred figure on the night stand. From the tape, they distinguish bells, a plane flying over, and the woman has a French accent and they hear a word in a foreign language for pig. From these clues, they figure it is possible for three places, all in Africa.

Edward goes to Africa and tracks down the room. The object they couldn't identify was a container holding a round glass object with a boat inside. Edward realizes it is his son who is the mole. He confronts Ed, Jr. and his son tells him he is in love with this woman. They are getting married. Edward tells him she is a spy for the Russians. He won't believe his father and leaves. Edward goes to the room next door. It is empty but he find evidence that some was there spying.

Edward meets with Ulysses. Edward tells him there is nothing left on his son and to leave him alone. Ulysses tells him that they are in love. She wants to marry Ed, Jr. Ulysses then tells Edward he will have to accept her into his family.

Edward goes to Africa as does Margaret. They are both waiting at the church with Ed, Jr. You then see the woman getting on a plane with a wedding dress. Halfway through the flight, she is thrown out of the plane. Ed, Jr. looks worried that she is not showing up. Edward looks at his son and tells him he loves him. Ed, Jr. asks his mother to in the church and then cries on his father's shoulders.

Edward knows there is a stranger in the house. He goes to Valentin's office and notices a book on the back table is not resting on the shelf. He pushes it down and reaches for the book next to it - a copy of Ulysses given to him by the british intelligence officer. Inside the lining of the book he finds a passport with Valentin's photo but another name. He goes to Valentin's home and asks him to play the violin. Valentin tells him its late and can't it wait. Edward insists on hearing him play now. Valentin plays the violin. Edward leaves and makes the comment that he wanted to see if there was something he told the truth about.

Edward then opens the dossier on Allen. He sends Allen a box of chocolates (which were a weakness of his) and it has a bank statement. He apparently was embezzling money. He resigns from his post.

Edward goes into a safe and pulls out a box. He then opens his father's suicide note. His father basically was ashamed for something he had done, regrets it and thought he would not shame his family any further.

He then is lead through a building being decorated by Hayes. It is the new CIA building.

The movie ends with Edward at CIA headquarters he will head one of the foreign intelligence and his fellow Skull and classmate Hayes will be its director.

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