Jack begins his career stationed in Berlin to work with Harvey Torriti (Alfred Molina), who is codenamed "the Sorcerer." Torriti takes Jack under his wing, and the two keep in touch even after Jack's career takes him from Berlin. A string of failed missions from Berlin to the Bay of Pigs Invasion forces Jack to conclude that the CIA has been severely penetrated by a KGB mole. The miniseries centers on the efforts of Jack and Harvey, along with the increasingly paranoid counterintelligence chief James Angleton (Michael Keaton), to expose and destroy the mole. Angleton becomes so paranoid he is forced to retire when he argues that evidence apparently exculpating a suspected mole was actually incriminating evidence because it was too easily discovered.
In 1954, Berlin is a hotbed of spies eager to put down cash in exchange for secrets. In the CIA station over a dingy cinema, Harvey Torriti (known as The Sorcerer) runs the Company's Soviet Russian division with his young apprentice Jack McAuliffe.
Jack had been recruited straight out of Yale, along with his best friend Leo Kritzky. Vishnevsky, an East German, has come to them with information that he wants to barter in exchange for safe passage for himself and his family to the West. Vishnevsky reveals that he has proof of the identity of a mole within MI6, the British intelligence service. When he hears this at the temporary headquarters of the burgeoning CIA in Washington, counterintelligence chief James Angleton sends orders to Berlin to begin Vishnevsky's exfiltration. As is his custom, Angleton shares this information with his best friend Adrian Philby, MI6's liaison to Washington.
Jack has been wondering whether Vishnevsky might have been feeding them misinformation but while he and the Sorcerer are waiting for the family, KGB agents and the Berlin police burst into the cinema downstairs. The CIA ops are able to make their escape but the defection has been compromised, proving the existence of the suspected mole.
At Yale, Jack and Leo had a third friend; Russian-born Yevgeny Tsipin. Yevgeny is doing graduate work at Yale when he is called back to Moscow to attend his mother's funeral. There, he is recruited for the KGB by master spy Starik, who has been watching Yevgeny for his whole life. Starik urges Yevgeny to follow in his father's footsteps by dedicating himself to the Soviet cause. While he is being trained in every aspect of American life, Yevgeny meets beautiful Azalia at Starik's dacha. Before Yevgeny leaves Moscow, Starik gives him an ultimatum – his country or the woman he loves. Yevgeny leaves for his assignment in the United States.
Hunting for the mole, Angleton conducts a thorough search of everyone in the CIA. When he comes up clean, he is led to believe that the defection has been blown by a leak somewhere in the Berlin operation. The Sorcerer is determined to prove him wrong. Meanwhile, the Sorcerer hands Jack his first full-scale assist; the handling of an East German ballerina named Lili, who can provide information from a figure known as The Professor, an important scientist in the East German hierarchy. Although the Sorcerer warns his young apprentice not to fall in love, Jack is smitten when he meets the beautiful dancer. The Sorcerer comes up with a plan to flush out the mole by feeding him real information, even though it means compromising one of his own operatives. When the cover is blown, they will know for sure. Jack, who is falling in love with Lili, has her followed to her apartment, which he bugs. He tries to convince Lili to give up spying and come to the West with him but she owes the Professor her life.
Yevgeny has arrived in Washington D.C. where he is posing as an American and working as a delivery boy for Khan's Liquor Store. He regularly communicates with Starik via an elaborate series of codes and numbers to get his orders. One of his regular assignments is to make liquor deliveries to the Georgetown home of Adrian Philby. In Berlin, the Sorcerer and Jack are ambushed by phony muggers and then "rescued" by phony cops who turn out to be KGB agents all part of the Sorcerer's plan to flush out the mole.
Jack's friend Leo Kritzky has fallen in love with Adelle Swett, a young woman whose influential father Phillip Swett is a personal friend of President Truman's. When Leo proposes marriage to Adelle, Phillip has him vetted and discovers that he works for the CIA. Despite this, he gives permission for Adele to marry Leo.
Discrepancies have been found between the information that Jack has been getting from Lili and the transcriptions of the surveillance tapes they have recorded of the Professor's conversations. When Jack confronts Lili with this, she tells him that she is the actual agent, forced into betraying the Professor by the KGB, who threatened both of their lives. She assures Jack, however, that her love for him is genuine.
The Sorcerer goes to Angleton's home in Virginia to tell him that his friend Philby has been a Russian spy for thirty years. He then argues his case against Philby to CIA Director Bedell Smith. When Angleton argues that Philby knows about Lili and the Professor and the CIA is still receiving information from them, the Sorcerer reveals that they are actually part of a KGB disinformation operation. Back in Berlin, Lili discovers that the Professor has hanged himself. As the Secret Police move in to arrest her, she shoots herself in the head. Since his associates Guy Burgess and Donald Maclean have defected, Philby is also recalled to Moscow. Before he leaves, Yevgeny tells Philby that he is not indispensable – the KGB has another mole already in place - Sasha. (NB: The adaptation takes liberties with both the historical record and Littell's novel, as Burgess and Maclean's defection to the USSR - and Philby's fall from grace in Washington - occurred in 1951. Philby did not defect to the USSR until 1963).
Two years pass. Jack has been sent to Budapest on the eve of the Hungarian revolution in order to get the freedom fighters to postpone their uprising. Dodging the AVH (the Hungarian Secret Police), he makes contact with Elizabet, a beautiful museum guide who leads him to the home of resistance leader Arpad Zelk in the hills outside of the city. Jack tells Arpad that if he encourages an uprising, the U.S. will not step in to help.
Jack is abducted and brought to the AVH prison where he is interrogated under torture. The Sorcerer has a contentious meeting with his KGB counterpart in Berlin, demanding the AVH release Jack (by virtue of the KGB's hold over AVH). By the time he regains consciousness, the revolution is underway. As Jack is being transported to a new location, Arpad and his lieutenants rescue him and then free Elizabet, who was also being held by the AVH. As the freedom fighters storm the AVH prison and kill all of the guards, Szabkanko, the commandant, begs Jack to protect him by revealing that he knows the identity of the mole within the CIA.
As Hungarian refugees pour into Vienna, Jack sends a message back to the CIA to back up the freedom fighters before the Russians return but President Eisenhower is adamant about not sending in troops to aid the Hungarians. Angleton insists that unless a lid is not kept on the president's intentions, thousands of Hungarians will die. The solution is to deceive the Russians with misleading radio traffic indicating a U.S. buildup of troops.
Jack joins the revolutionaries as the Russian tanks begin rolling into Budapest. He, Elizabeth and Zoltan, another rebel, join Arpad at the Killian Barracks, where hundreds of demonstrators are taking shelter. Realizing that further resistance is futile against the Russians, Arpad leads a straggly procession of wounded fighters through the outer walls, where they are brutally gunned down. Jack, Elizabet and Zoltan escape through a series of tunnels in the subbasement of the barracks. They make their way to the Austrian border where the checkpoint is being monitored by the Sorcerer and other CIA representatives, who spot Jack among the throng. At the refugee camp, Jack re-unites Elizabet with her 10-year old daughter (whose father was Arpad).
Four years later, Jack is in the Guatemalan jungle, where Cuban rebel leader Roberto Escalona is training a group of volunteer émigrés in preparation for an invasion of their homeland after a landing at the Bay of Pigs. Roberto believes that President Kennedy will send in the Navy to help the rebels but Jack reminds him that if his group gets into any trouble once they land on the beach, they're on their own. The Sorcerer has his own plans for Fidel Castro which involve calling on his Mafia contacts to arrange an assassination. Through a Brooklyn mobster, the Sorcerer is led to Chicago mob boss Sam Giancana who comes up with the idea of poisoning Castro via one of the chocolate milkshakes that the dictator is served every afternoon at the Hotel Libre in Havana.
In Washington, Yevgeny is nearly arrested by the FBI but is able to construct a new American identity for himself. He gets word to his handler - Sasha – who has vital information about the Cuban invasion to impart to Starik. In the CIA war room, Angleton argues that the Company has no business getting involved in Cuba. As long as Sasha is still operating, all of their vital information is being funneled to the enemy and the operation is doomed to failure. His associates, including Richard Bissell, the architect of the invasion plan, scoff at the notion that Sasha exists at all. In Havana, the head of Castro's Secret Police intercepts the waiter who is planning to serve the poisoned milk shake to Castro and has him drink it instead.
Jack is part of the first wave of rebel fighters arriving at the Bay of Pigs. Although the landing site has been changed, they set up makeshift headquarters on the beach, becoming sitting ducks for the tanks and aircraft that Castro is planning to send in. As the Cuban Sea Fury planes appear overhead, raking the shoreline with machine gun fire, Roberto is desperately expecting the U.S. air cover that never comes. JFK has resolutely refused to commit air forces to combat. Roberto urges Jack to swim to safety aboard a U.S. destroyer in the bay – if Castro takes him, he will tell the world that the raid was led by American officers. Jack leaves Roberto and the rebels on the beach to face certain death. Angry at the president and the Company for letting the rebels down, Jack contemplates handing in his resignation. His old friend Leo talks him out of it and Jack is awarded with the Agency's highest honor.
Fourteen more years pass. It is now 1974. Jack and Leo, who has climbed so high at the Company that he is being talked about as the next director, are in their forties. Jack is working on the case of Krushkin, a KGB captain who wants to defect with his family. In exchange, he will provide more information about the elusive Sasha, with whom Angleton has become increasingly obsessed. Angleton thinks that it may be a trick of Starik's but Jack assures him that he believes that Krushkin is credible.
Using a liquor delivery list from Khan's store, Angleton narrows the names down to Company employees, leading him to Leo Kritzky. Returning with his wife from a vacation in France, Leo is arrested at the airport and brought to a holding cell where he is strip-searched and then interrogated by Angleton. As he looks on from behind a two-way mirror, Jack is reeling from the possibility that his best friend may be responsible for Lili's suicide and the deaths of the Cuban rebels and the Hungarian freedom fighters. Jack is shocked by Leo's condition when he visits him in prison. Still insisting that he is not Sasha, Leo tells Jack that he believes Krushkin has been dispatched by the KGB. But Krushkin mysteriously returns to the Soviet Union, where he is put on trial for treason and shot. Jack and the Sorcerer don't believe it and when it turns out that Krushkin is alive after all, Leo is cleared and returns to his office at the Company. Angleton remains convinced that Leo is Sasha and is forced to resign; in his parting words to the Company, he reels off a list of international statesmen (including Averell Harriman and Henry Kissinger) he believes are under KGB control as part of a massive scheme to convince the US that it is winning the Cold War and turn the world against it.
As the Cold War winds down in 1987, improvements in technology have enabled the counterintelligence analysts to pinpoint the telephone number that Moscow Radio broadcast in the early 1950s to its KGB operatives. It leads to Khan's Liquor Store and to Yevgeny. Jack visits the dying Angleton who figures out that lists of further numbers broadcast by Moscow are not telephone numbers but bank accounts, part of a complicated financial scheme designed by Starik to wreak havoc on the American economy. Angleton again accuses Leo of being Sasha. Jack starts to have his own suspicions but is not prepared when he accompanies the FBI to arrest Yevgeny and discovers that it is his old classmate from Yale. Jack then pays a visit to Leo – to whom Yevgeny had been making deliveries over the years – and accuses him of being Sasha. Leo does not deny it – he admits to being recruited to the KGB by a girlfriend who took advantage of his Socialist leanings (learned from his father) – and shoots Jack in the gut. Before he disappears into the night, Leo phones for an ambulance for his friend.
While Jack is in the hospital recovering, Starik's financial plot is curtailed by the Company, but not altogether avoided. When he is released, Jack pays a visit to Angleton, who has been proved right about Sasha and was instrumental in identifying Starik's agents in banks around the world.
Several years later, the collapse of the Soviet Union is imminent. Yevgeny has been in prison but Jack (now 64) offers him an early release if he will provide the whereabouts of Leo. He reveals to Yevgeny that his great love Azalia was exiled to the gulag by Starik, after which Yevgeny is happy to oblige. He tracks down Leo in Moscow but warns him before passing his whereabouts to Jack. He visits a senile Starik in hospital and is reunited with Azalia, now a writer.
Jack is in Moscow, appraising the Company of the prospects that Boris Yeltsin will take power and bring democracy to Russia. Planning to kill, Jack has his own men follow his old friend and arrange for him to be run down; however, faced with pushing Leo in front of the car himself, Jack chooses not to, disappearing into the crowd just as Leo realises he is there. Back in Maryland, the Sorcerer and his apprentice Jack discuss their work in the Cold War. Jack expresses his misgivings over the things they did at the Company, but Harvey assures him they were the "Good Guys" because they won.
Michael Keaton, Chris O'Donnell, and Alfred Molina were all previous stars of comic book superhero films; Keaton portrayed Batman in Tim Burton's Batman and Batman Returns, O'Donnell portrayed Robin in Joel Schumacher's Batman Forever and Batman & Robin, and Molina portrayed Doctor Octopus in Spider-Man 2.