Deep Throat

This elusive, mysterious, and sometimes duplicitous informant knew much about Mulder's work. He was deeply entrenched in the Syndicate's dealings and his information was meant to hinder Mulder through disinformation as often as it was given to help him uncover the truth.

Scott Ostelhoff
Scott Ostelhoff is a Department of Defense agent working for the Syndicate. He is assigned to watch Mulder as the fake alien plot is hatched (Gethsemane). His body is mistaken for that of Mulder's after he is shot in the face.

Quiet Willy

This Syndicate minion is assigned to assassinate Cigarette Smoking Man by the First Elder. He is also instructed to take Cassandra Spender to the abductee gathering site, and he ends up being burned to death by an alien rebel.

Surgeons
These Japanese scientists continued Nazi war experiments designed to create an indestructible human-alien hybrid (Nisei). The scientists are murdered, and Mulder suspects that the U.S. government is responsible

Section Chief Joseph McGrath

After Mulder secretly infiltrates the government cover-up of a UFO crash, McGrath decides to fire Mulder and shut down the X-Files. He is overruled by Deep Throat, who tells McGrath to keep his friends close . . . and his enemies closer (Fallen Angel).

William Mulder
Mulder's father had long-standing ties to the Syndicate. He was involved in the cover-ups while at his job at the State Department. He is murdered by Krycek when he tries to tell Mulder the truth about his own involvement.

X

This mysterious man is working for the Syndicate, but supplying Mulder with information as well. It is unclear how far he can be trusted, as he has misinformed Mulder on many occasions. He has no qualms about using Mulder to further his own agenda. After his link to Mulder is discovered, he is shot to death by the Syndicate.

Senator Sorenson

This Senator chairs the Senate Subcommitte to which Mulder and Scully must explain their actions (Tunguska/Terma). Scully refuses to divulge Mulder's location, and Senator Sorenson has her jailed for contempt of Congress. Sorenson is a puppet for the Syndicate, and he thwarts the agents' attempts to find the truth at every possible opportunity

Dr. Charne-Sayre

This virologist is working on the Black Cancer cure for the Syndicate, and she is also the personal physician of the Well Manicured Man. In order to study the disease, she infects some elderly patients in a nursing home. Her experiments are cut short when she is assassinated by Vassily Peskow in the WMM's stables (Tunguska/Terma).

Purity Control

The agents discover that Purity Control is the code name for an extraterrestrial bacterial virus that is lethal in nature (Erlenmeyer Flask). This research, headed by Dr. Berube, is covertly funded by shadowy factions of the U.S. government. Berube is assassinated when his conscience gets the better of him and he tries to warn people about the nature of the Purity Control virus.

Black Cancer

The Russians infect hundreds of people with a deadly virus, known as the Black Cancer, a black oil that congeals into tiny worms which penetrate the skin. Once infected, these unwitting lab rats are given an injection of what is hoped to be a cure for the
deadly disease.

Louis Cardinal

This hired assassin, also known to be a cohort of Alex Krycek, is responsible for the murder of Scully's sister, Melissa, as well as attempting to assassinate Skinner. Upon being arrested, he conveniently commits suicide while in custody