Plot
In 1961, the Bay of Pigs invasion ends disastrously. Senior CIA officer Edward Wilson is warned of a possible "mole" in his department. Returning home, he finds a photograph of a man and woman in bed, as well as audio tapes that have been tampered with.
In 1939, Wilson attends Yale University and is invited to join the Skull and Bones secret society. During his initiation, he reveals that he discovered but never read the suicide note left by his father Thomas, an admiral in line to serve as Secretary of the Navy until his loyalties were questioned.
FBI agent Sam Murach recruits Wilson to investigate his poetry professor Fredericks, a suspected Nazi sympathizer. When exposed, Fredericks resigns. Wilson begins dating Laura, a fellow Yale student who is deaf. After learning that World War II has begun in Europe, Laura asks Edward to sleep with her but panics at the last moment.
In 1940, Wilson attends a party and meets Margaret "Clover" Russell. He is also introduced to General Bill Sullivan, who tells him the US will soon be compelled to enter the war and offers Edward a job in foreign intelligence. Margaret makes aggressive advances on Edward, to which he succumbs.
While at the beach with Laura, Edward is approached by Margaret's brother John, who tells him she is pregnant and implies that Edward is obligated to marry her. Laura, reading their lips, walks away. On Edward and Margaret's wedding day, Edward is given orders to leave for London.
In London, Edward is reunited with Dr. Fredericks, a British intelligence operative who had recommended Edward for counterespionage training. Intelligence officer Arch Cummings informs Edward that Fredericks's indiscreet homosexual liaisons pose a security risk because they make him susceptible to blackmail. Fredericks refuses to retire quietly and is assassinated.
In post-war Berlin, Edward collaborates with his Soviet counterpart "Ulysses" in the exchange of captured scientists. During a phone call home, his son Edward Jr. inadvertently reveals that Margaret is having an affair. Edward impulsively sleeps with his office's interpreter, Hanna Schiller, but discovers that she is a Soviet operative, which results in her murder.
In 1946, Edward returns to Washington, DC and a distant Margaret. Both admit to their respective affairs. Edward is approached by Sullivan to help create the CIA with colleague Richard Hayes, under director Phillip Allen.
While Edward feels genuine affection for his son, Margaret grows increasingly disenchanted as he continually prioritizes work over family.
Valentin Mironov, a high-ranking KGB defector, presents information about "Ulysses." While attending a play with Mironov, Edward encounters Laura, and they begin an affair. Margaret receives compromising photographs of them and publicly berates Edward.
Another Soviet defector claims to be the real Mironov and accuses the first defector of being a double agent. Beaten, waterboarded and administered liquid LSD as a truth serum, he ridicules his interrogators and hurls himself out a window.
Edward Jr. follows his father's footsteps in attending Yale and joining Skull and Bones. To Edward's surprise, his son expresses interest in joining the CIA, which Margaret opposes. During an argument, Edward admits he only married Margaret because she was pregnant. Margaret begs him to protect their son, which he promises to do.
During another party, Edward Jr. overhears his father discussing the upcoming Bay of Pigs invasion. Realizing this, Edward reminds his son of the importance to remain silent. Margaret tells Edward she is leaving him.
In 1961, the CIA conducts a reconstruction of the tape recording, which appears to have been made in the Democratic Republic of Congo. Traveling there, Edward encounters "Ulysses," who plays an intact recording: Edward Jr. reveals the Cuban operation to his lover Miriam, who is a Soviet operative. "Ulysses" offers to protect Edward Jr. if Edward becomes a double agent. Edward confronts his son, who refuses to believe that Miriam is a spy and reveals that he asked her to marry him.
Edward discovers evidence that Mironov is a double agent, with Arch Cummings as his co-conspirator. Meeting with "Ulysses" a final time, Edward declines his offer but implicitly agrees that Miriam, although genuinely in love Edward Jr., is a threat to both sides. En route to her wedding, Miriam is thrown from a plane and killed. A devastated Edward Jr. reveals she was pregnant.
Philip Allen resigns in disgrace after Murach uncovers evidence that he has been embezzling money for years. The President names Hayes as the new CIA Director, and he appoints Edward to be the agency's inaugural head of CIA counter-intelligence.
Edward finally reads his father's suicide note in which he admits to being a traitor, begs his family's forgiveness, and urges his son to live with decency and truth. Edward burns the letter. The film ends with him moving into his new offices at the CIA.
