Agent Fox William Mulder: Agent Mulder's obsession with alien abductions & paranormal began when his sister, Samantha, was abducted when they were children. He has recently been fired from his position in the FBI, he is currently at large after escaping a military prison cell Agent Dana Katherine Scully: Mulder's partner on the X-Files, who was assigned to work with him by former FBI section chief Blevins. She's a medical doctor and instructor at the FBI Academy. Her current whereabouts are unknown but is most likely accompanying Fox Mulder. Agent John Doggett joined the FBI after serving in the NY Police Dept & the Marine Corps. He was assigned to find Mulder by Deputy Director Kersh. He is now patnered with Agent Reyes on the X-Files. Assistant Director Walter Skinner: Mulder and Scully's supervisor in the FBI. He frequently has worked to assist them with the X-Files and to try to protect them on occasion. The Cigarette Smoking Man: A mysterious figure involved in a multi-national conspiracy to create human/alien hybrids. His son, Jeffrey Spender, was an FBI agent. Jeffrey's mother was an alien abductee. One of his aliases over the years was as C. G. B. Spender. He is assumed to have died in the ruins of an Anasazi pueblo. Alex Krycek: A former FBI agent who had been temporarily assigned to work with Mulder during season 2. Krycek was really a spy working for the Cigarette Smoking Man. He was recently killed by a gunshot to the head. Ringo Langly: One of the Lone Gunmen, a trio of conspiracy theorists. Langly is the group's communications and computer expert. The Lone Gunmen died from being exposed to a biochemical weapon. John Fitzgerald Byers: One of the Lone Gunmen, a trio of conspiracy theorists. Byers is a former government employee and has scientific knowledge. The Lone Gunmen died from being exposed to a biochemical weapon. Melvin Frohike: One of the Lone Gunmen, a trio of conspiracy theorists. He is the group's surveillance specialist. The Lone Gunmen died from being exposed to a biochemical weapon. Deep Throat: An informant involved with the Cigarette Smoking Man in the conspiracy. He assisted Mulder and Scully with secret information during the first season before being shot trying to rescue Mulder. X: Another informant of Mulder's. X, rather than assisting Mulder like Deep Throat, was more of a manipulator. He was killed by an alien bounty hunter at the end of the 4th season. The Well Manicured Man: The leader of a multi-national conspiracy to create human/alien hybrids. He was killed in an explosion in the X-Files feature film. Agent Jeffrey Spender: The Cigarette Smoking Man's son. He's an FBI agent that, along with Agent Fowley, replaced Mulder on the X-Files during season 6. His mother, Cassandra Spender, is an alien abductee, but Agent Spender is a skeptic. He was shot by his father and later subjected to medical experiments which left him horribly disfigured. Agent Diana Fowley: A former partner and love interest of Agent Mulder back when they started the X-Files. She was working for the Cigarette Smoking Man but was killed after she betrayed him.

Deputy Director Alvin Kersh: The FBI's new Deputy Director assigned John Doggett to lead the search to find Mulder. A true skeptic of the X-Files and alien conspiracies, he frequently butts heads with agents involved in the X-Files cases.