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Doggett served in the United States Marine Corps in the 24th Marine Amphibious Unit from 1977 to 1983. His final rank was Sergeant (E-5). While serving in the military, he became good friends with fellow Marine Knowle Rohrer. From 1982 to 1983, Doggett played a role in the Multi-National Peacekeeping Force in Lebanon. He served during the 1983 Beirut barracks bombings. Doggett retired from the U.S. Marine Corps with commendations after being wounded in the line of duty. After gaining a Juris Doctor and a Master's degree in Public Administration from Syracuse University, Doggett went on to work for the New York Police Department from 1987 to 1995, eventually becoming a detective in the Fugitive Division's Warrant section. While he was working for the NYPD, his son, Luke Doggett (played in flashbacks by Jake Fritz), was abducted and murdered. Doggett teamed up with Special Agent Monica Reyes, who was working out of the New York City FBI field office at the time, to search for his son's killer. After his son's death, Doggett's marriage to Barbara Doggett (played by Patrick's real-life wife Barbara) ended in divorce.

In 1995, Doggett graduated from the FBI Academy and assumed the position of FBI Special Agent in the Criminal Investigations Division. In 2000, Agent Doggett was assigned by Deputy Director Alvin Kersh to head up the manhunt to find Special Agent Fox Mulder. The manhunt was unsuccessful and Doggett was demoted to work on the X-Files with Special Agent Dana Scully. During this time, Doggett and Kersh developed a bitter enmity, similar to the early relationship between Mulder and Walter Skinner.

Initially, Scully and Doggett were not very trusting of each other. After years of investigating several X-Files cases with Mulder, Scully had slowly grown to believe in the existence of the paranormal. Doggett, however, is a no-nonsense agent, who frequently utilizes his down-to-earth sensibilities he learned as a Marine and a cop. Doggett therefore functioned as "the skeptic", while Scully somewhat served in Mulder's old position of "the believer". Gradually, Doggett and Scully came to trust one another to some degree, although he and Mulder, who later returned and recovered from his abduction, remained untrusting of each other for some time. Doggett and his new partner, Reyes, took charge of the X-Files after Mulder was fired from the FBI and Scully left active duty to teach at the FBI Academy and to care for her son, Baby William. In the series finale, Doggett testified on Mulder's behalf when Mulder was charged with murder. Later, he and Reyes narrowly escaped from Knowle Rohrer, who Doggett had discovered about a year prior was working for the conspiracy. At the end of the series, Doggett is likely a regular agent, as it appears that Kersh was forced to close down the X-Files division.

Doggett does not appear, nor is he mentioned, in the 2008 X-Files feature film. He similarly does not appear or is mentioned in the 2016 television revival of The X-Files.