Agts. Mulder and Scully were summoned by Frohike to the office of the Lone Gunmen. Frohike was excited and highly anxious. Byers and Langly had performed thorough sweeps of the room, but Frohike refused to speak until countermeasure filters were activated to interfere with any possible bugging device. Frohike then disclosed to Agts. Mulder and Scully that he was on the verge of uncovering not only the identity but also the history of the man referred to as the Cigarette-Smoking Man. As Frohike related the story of the Cigarette-Smoking Man’s life, the Cigarette-Smoking Man himself was listening from a decaying, rat-infested loft nearby. The Cigarette-Smoking Man had no difficulty defeating the Lone Gunmen’s filters. He assembled a high-powered rifle and targeted the doorway of the Lone Gunmen’s office. He lit a Morley cigarette with a lighter inscribed "Trust no one."

Frohike told Agts. Mulder and Scully that the Cigarette-Smoking Man was born on August 20^th, 1940, at the moment Leon Trotsky was assassinated by a Stalinist agent. According to Frohike, the Cigarette-Smoking Man’s father was a Communist activist who had spied on the United States and been executed under the Espionage Act before the Cigarette-Smoking Man was able to walk. The Cigarette-Smoking Man’s mother died of lung cancer before the Cigarette-Smoking Man could speak. He became a ward of the state, a loner who enjoyed reading. Frohike added that in 1962 the Cigarette-Smoking Man was a Captain in the United States Army, stationed at Fort Bragg, North Carolina. At Fort Bragg, the Cigarette-Smoking Man was a bunkmate of Agt. Mulder’s father Bill Mulder.

At one point, the Cigarette-Smoking Man was summoned to a meeting with a General Francis. Also attending were an unidentified organized crime figure, an unidentified Cuban, and an unidentified federal agent. The agent put the Cigarette-Smoking Man on display for the others, listing a series of covert actions in which the Cigarette-Smoking Man had apparently taken part, including the assassination of Patrice Lumumba and the training of Cuban nationals for the Bay of Pigs operation. During the meeting, the Cigarette-Smoking Man was offered a cigarette, but at the time he was a non-smoker so he declined it. General Francis discussed the Cigarette-Smoking Man’s father as an example of an evil but extraordinary person. He suggested that the Cigarette-Smoking Man might also have extraordinary qualities, which should be put to use against Communism. He assigned the Cigarette-Smoking Man a task of the utmost importance, the assassination of President Kennedy. He assured The Cigarette-Smoking Man that an appropriate patsy had been found for the action. He indicated that accepting the assignment would require the termination of The Cigarette-Smoking Man's standing as an officer and that all records of his service would be eliminated.

In Dallas, Texas, the Cigarette-Smoking Man, calling himself Mr. Hunt, and posing as a pro-Cuba communist gun-runner, elicited the loyalty of Lee Harvey Oswald. Early on the morning of President Kennedy’s visit to Dallas, the Cigarette-Smoking Man gave Oswald a rifle to stash on the sixth floor of his place of employment, the Texas School Book Depository. The Cigarette-Smoking Man assured Oswald that as soon as the rifle was taken from the Depository by another pro-Cuba communist, Oswald would find a Cuban visa and travel money in his rented room. The Cigarette-Smoking Man made sure to mention his own plan to see a movie at the Texas Theater that afternoon. Oswald received carfare from the Cigarette-Smoking Man, handing the Cigarette-Smoking Man his cigarettes, which the Cigarette-Smoking Man put in his pocket.

Before starting work that day, Oswald hid the rifle behind crates in the Book Depository. As President Kennedy’s motorcade approached, other Depository employees watched the proceedings from windows on the fifth floor. Oswald did not view the motorcade, but went to a soda machine in the Depository commissary. The Cigarette-Smoking Man, meanwhile, entered the sewer system through an overflow tunnel and positioned himself in a sewer under Dealy Plaza. When the motorcade passed the Depository, the Cigarette-Smoking Man fired twice, killing the President Kennedy. Oswald saw police enter the Depository and run toward the sixth floor. He realized that he had been set up. Oswald proceeded to his rented room, where he retrieved his .38 caliber snub-nose pistol. Confronted on 10^th Street and Patton by an uniformed police officer, Oswald shot the officer. In search of the Cigarette-Smoking Man, Oswald proceeded to the Texas Movie Theater. A showing of an Audie Murphy picture was interrupted by the arrival of police officers, who arrested Oswald. Observing the proceedings from a seat in the theater, the Cigarette-Smoking Man smoked his first cigarette, one from Oswald’s pack of Morley’s.

Frohike continued by telling Agts. Mulder and Scully of the Cigarette-Smoking Man’s activities in 1968. On the day the Cigarette-Smoking Man finished writing an adventure novel entitled Take a Chance: a Jack Colquette Adventure, he heard Dr. Martin Luther King, Jr., on the radio, endorsing Communism. Soon afterward, the Cigarette-Smoking Man attended a meeting regarding a top-secret report entitled "Operation Chaos." That meeting was also attended by the Bureau Director and other Bureau and military personnel. Its subject was King’s endorsement of third-world Communism and the possibility of a Negro war on the United States. The Cigarette-Smoking Man expressed his admiration for King. He also expressed his belief that King’s Communism had made him dangerous. The Cigarette-Smoking Man harshly criticized the ineffectiveness of the Director’s ongoing attempts to discredit Dr. King. When the Director’s aide announced that the Director was leaving, the Cigarette-Smoking Man curtly ordered the Director to stay. The Director complied. The Cigarette-Smoking Man explained that as he had too much respect for King to order him killed, he would assassinate King himself. He would disguise the assassination as racially motivated by finding a white Southerner to be the patsy.

In Memphis, the Cigarette-Smoking Man stood outside the theater where King was speaking and smoked a Morley, listening to King’s last speech. At a motel, the Cigarette-Smoking Man, posing as a criminal gun dealer, sent his employee James Earl Ray to get a 30.06 rifle and a pair of binoculars. Then he sent Ray to a movie. The Cigarette-Smoking Man left the rifle and binoculars with Ray’s fingerprints and proceeded to the Lorraine Motel, where he shot and killed King. Shortly later, the Cigarette-Smoking Man’s novel, which he had written under the name Raul Bloodworth, was rejected by a publisher. This would be the first in a long series of rejections. On the night of the rejection, listening to Robert F. Kennedy quote Aeschylus on television, the Cigarette-Smoking Man looked at the picture of Bill Mulder’s wife and child which he had taken in 1962.

Frohike then related for Agts. Mulder and Scully the Cigarette-Smoking Man’s activities since 1991. On Christmas Eve, 1991, the Cigarette-Smoking Man met with his operatives Lydon, Matlock, Jones, and Cook. In an attempt to give up smoking, the Cigarette-Smoking Man was wearing a nicotine patch. The operatives reported outcomes of many of the Cigarette-Smoking Man’s plans, which ranged from moving the Rodney King trial to preventing the Buffalo Bills from ever winning the Super Bowl. During the meeting, a call came from Saddam Hussein; the Cigarette-Smoking Man curtly ordered Saddam to call back. Jones raised the issue of Agt. Mulder having gained access to the X-Files and predicted possible trouble. The Cigarette-Smoking Man told Jones that Agt. Mulder was the Cigarette-Smoking Man’s to watch. News came of Gorbachev’s resignation. The operatives referred to the fact that the United States now had no enemies. Invited by Lydon for Christmas, the Cigarette-Smoking Man declined. He gave his operatives Christmas presents of identical ties and adjourned the meeting. After the meeting, the Cigarette-Smoking Man walked by Agt. Mulder’s office in the basement of Bureau Headquarters.

At home that night, the Cigarette-Smoking Man began writing a new novel. The novel opened with an expression of yearning for a second chance. The Cigarette-Smoking Man’s writing was interrupted by an urgent call from Deep Throat. The Cigarette-Smoking Man and Deep Throat met at a warehouse in the Yew Mountains of West Virginia. A living Extraterrestrial Biological Entity (E.B.E.) had been salvaged from the wreckage of an alien spacecraft. As the Cigarette-Smoking Man and Deep Throat walked toward the room where the E.B.E. was being kept alive, they discussed the threat posed by the crash’s timing. The Cigarette-Smoking Man reminded Deep Throat that the story of the Roswell landing, which the two of them had concocted, was becoming successful in its mission of misleading the public. Deep Throat reported that the Russians had tracked the alien spacecraft’s entry and pinpointed its touchdown. In the life-support room, the Cigarette-Smoking Man pointed out that evidence of a living E.B.E. would advance Bill Mulder’s project by decades. Deep Throat referred the Cigarette-Smoking Man to Security Council Resolution 10-13, which states that any country capturing such an entity is responsible for its destruction. The Cigarette-Smoking Man and Deep Throat flipped a quarter to decide who would shoot the E.B.E. Deep Throat lost. As the Cigarette-Smoking Man removed his nicotine patch, Deep Throat shot the E.B.E.

Frohike continued that it was shortly after the assassination of the E.B.E. that Agt. Mulder’s work on the X-Files had begun to draw attention from the Cigarette-Smoking Man. It was at that time that Agt. Scully had been assigned to work with Agt. Mulder. The Cigarette-Smoking Man had eavesdropped on the first meeting of Agts. Mulder and Scully. As Frohike concluded his report to Agts. Mulder and Scully, in the loft across the street, the Cigarette-Smoking Man loaded the rifle he had aimed at the offices of the Lone Gunmen. Agt. Mulder asked Frohike how he had learned the information about the Cigarette-Smoking Man. Frohike told Agts. Mulder and Scully that to the Cigarette-Smoking Man’s surprise, his novel Second Chance had been accepted by Pivotal Publishing. The novel told the thinly fictionalized story of the Cigarette-Smoking Man’s life. Pivotal Publishing editor Walden Roth told the Cigarette-Smoking Man that Pivotal would serialize the novel in their magazine Roman a’ Clef.

The Cigarette-Smoking Man, excited by this realization of a lifetime ambition, wrote a letter of resignation to the government. When he bought the magazine at a newsstand, however, the Cigarette-Smoking Man learned that Roman a’ Clef is a pulp-pornography magazine. The story was advertised as a "Cold War barn burner," and the end of the story had been rewritten. The Cigarette-Smoking Man bought a pack of Morley’s. Sitting on a bench beside a homeless scavenger, the Cigarette-Smoking Man expressed his belief that life is as disappointing as a box of chocolates. He tore up his letter of resignation. After the Cigarette-Smoking Man left the bench, the homeless person began reading the magazine.

Frohike told Agt. Mulder that when he had read the story in Roman a’ Clef, it had seemed familiar. Frohike promised to check the story further with a source who could provide definitive evidence. Frohike emerged from the office of the Lone Gunmen into the Cigarette-Smoking Man’s scope. The Cigarette-Smoking Man, however, refrained from killing Frohike.