The Syndicate is an organization seen in The X-Files described as "a consortium that represents global interests." Because of their involvement in the coverup of extraterrestrial visitation, they were an enemy of the X-Files investigators during the first six seasons of the series. The Cigarette Smoking Man was a prominent member.
A pure embodiment of the "shadow government" of conspriacy theory lore, the Syndicate are comprised of government officials, wealthy businessmen, and high level mafia kingpins. Since 1990, they have been led by a German aristocrat named Conrad Strughold. With the exception of the British Well-Manicured Man and the Italian First Elder, they are primarily American. Most of their meetings are held in an upmarket club located on West 46th Street in New York City and do not involve Strughold. Meetings involving Strughold, who is not legally able to enter the United States, are held in London.
According to the Well-Manicured Man, the Syndicate formed at the end of World War II, when German scientists who were working on an alien-human hybrid defected to the United States. A man known as Deep Throat claimed that it began when the United States, the Soviet Union, the British Empire, China, France, West Germany, East Germany, and the smaller nations of Western Europe signed a treaty that if an alien spacecraft crashed on Earth and its extraterrestrial survived, the country that held them would be responsible for their extermination. In any case, they learned that extraterrestrials (actually Earth's original inhabitants) were planning to slowly colonize the planet, resulting in a full scale takeover in 2012, with the aid of a virus known as "Purity" or "Black Cancer." The original incarnation of the Syndicate sought to prevent this, while also keeping it secret from the public eye. The incarnation of the Syndicate seen in the series likely formed in the late 1960s, as these men are too young to have fought in World War II. By 1973, all attempts to create a vaccine for the Black Cancer had met with failure. The Soviets were planning on developing their own vaccine while sabotaging American efforts, raising the stakes of the Cold War. In any case, the Syndicate decided to join forces with the "Colonists," if only to stall for time. They offered up their heirs as collateral, under the assurance that they would survive. Unfortunately, in the years that followed the Syndicate was corrupted, and some members, such as William Mulder, Alvin Kurtzweil, and the aforementioned Deep Throat, grew disenchanted at the power plays and internal struggles.
Deep Throat would eventually feed some information about the conspiracy to FBI Agent Fox Mulder (William’s son), while simultaneously protecting other interests. However, his betrayal was eventually revealed and he was subsequently assassinated by a Syndicate hitman in the season 1 finale, “The Erlenmeyer Flask”. The Syndicate wanted to kill Mulder as well, but the Cigarette Smoking Man convinced most of them that that killing him would make him a martyr.
In season 2, the Cigarette Smoking Man assigns Alex Krycek to spy on Mulder. Deducing that Mulder’s partner, Dana Scully, was a bigger problem than they realized, Krycek and the Cigarette Smoking Man arranged for Scully to be abducted by the Colonists. She was returned a few months later with no memory of where she had been. In the season 2 finale, "Anasazi", the Syndicate was sent into a panic when a computer hacker known as The Thinker downloaded the Majestic 12 files onto a DAT. This prompted William to come clean to his son about his involvement in the conspiracy, but he was killed by Krycek before he had the chance. The Thinker was killed soon after.
At the start of season 3, the Syndicate Elders make their first actual appearance. The Cigarette Smoking Man is under pressure from them to retrieve the DAT and contend with Scully, who is asking too many questions about her abduction. Krycek is able to steal the DAT, but he fails to kill Scully, accidentally killing her sister, Melissa, instead. Determined to distance himself from Melissa’s murder, the Cigarette Smoking Man attempted to kill Krycek with a car bomb. He survived, and with the DAT in his possession became a free agent.
In season 4, Krycek is working for the Russians. Using retired KGB assassin Vassily Peskow as his agent, he destroys much of the Syndicate's Black Cancer research. The Elders decide to take the Cigarette Smoking Man “out of the loop” for his failure to prevent this. The Cigarette Smoking Man figures this out at the start of season 5, but it is too late, as the Elders have decided to assassinate him. Unbeknownst to them, he survived the attempt and fled to Quebec.
Later on in season 5, it is discovered that the Russians have developed a vaccine against Purity/Black Cancer, although it is very weak. Krycek steals the vaccine and eventually gives it to the Well-Manicured Man. He is then welcomed back into the Syndicate. It is also around this time that a group of rebels opposed to the Colonists emerge. The Well-Manicured Man sees this as a sign that resistance against the colonists is possible, and suggests siding with the Rebels. He is overruled by the other Elders. Soon after, the Elders discover that the Cigarette Smoking Man is still alive, and still needed. He is brought back from the cold, both sides willing to forgive and forget.
In the movie, the Elders learn the truth about the virus: it is actually a parasite that kills its host and subsequently mutates into a new lifeform. Shocked by this knowledge, the Well-Manicured Man gives the vaccine to Mulder, then commits suicide, realizing that his life would be over once the Syndicate discovered what he had done.
In season 6, the Syndicate succeed in creating an alien human hybrid, and as per the 1973 agreement, travel to El Rico Air Force Base to deliver her to the Colonists. When they arrive, they are instead met by the Rebels, who surround and incinerate them. The Cigarette Smoking Man, Krycek, and Strughold manage to avoid this terrible fate.
Strughold is presumably still alive by the end of the series, so it is possible he may continue the conspiracy in future entries of the film series.