With the 1973 agreement, the Syndicate had agreed to cooperate and not resist the alien Colonists. Those who would be saved in the end would only be the members of the Syndicate and their families. But from the beginning there were voices of dissent: not to cooperate, to resist until the very end, to try to save everyone, the world. It was William Mulder's idea to try and develop a vaccine that would protect a human from the Black Oil, that would kill the Black Oil once it entered the body of an inoculated human. In a war that was to be biological, a vaccine would be they key to survival.

With the majority vote of 1973, the Syndicate chose collaboration. But Bill Mulder still held on the idea, and his project survived in the mind of the conspirators as a way out that could be handy when the time would come. As much as the collaboration with the aliens was a secret from public and government, any research for a vaccine would be even more secret as it would have to be done without the aliens' knowledge. If the Colonists were to know of this, the agreement would be broken and the conspirators exterminated.

Thus progress towards a vaccine was slow: officially, priority was given to the hybridization research. The strategy the Syndicate chose to follow was to do the Colonists' bidding but to deceive them in secret. The hybridization program was never allowed to succeed: research was done, but every time it came too close to obtaining the successful gene therapy hybrid, the work was destroyed and colonization was stalled. This bought precious time for the development of a vaccine, the true goal in which few people ended up believing in.

What the vaccine research lacked most was source material. Alien tissue and biological material was mainly used with the hybridization experiments, and what a vaccine program needed most was crude Black Oil in its primeval form. That, the Syndicate didn't have, and its knowledge of Black Oil remained very basic for a long time.

The Syndicate was a thing of the West; the USSR was necessarily left out during the Cold War. Some time in the 1980s, geological surveys in Tunguska led to the discovery of the weakened, coma-inducing Black Oil trapped in the rocks. The Russians started extracting this "Black Cancer" from the Tunguska rocks: using any workforce available (local population, prisoners), they built a gulag in the vicinities of the mining works and made it a center for biowarfare research. Soon enough, they were able to use Black Cancer as a biological weapon. They provided to Iraqi leader Saddam Hussein; its efficiency was proven on US troops during the Gulf War.

In order to protect their own soldiers, the Russians started searching for a cure for the Black Cancer. The same workforce that was used to mine Black Oil-rich rock was used as test subjects for the experiments to develop a vaccine against this Black Oil. Benefiting from a weakened form of the alien virus and a limitless number of prisoners, all in a remote place of the globe, the Russians were able to make progress. After sacrificing hundreds, perhaps thousands, of their prisoners, by 1998 they had a treatment that was in no way a vaccine but it was effective enough.

For cataloguing their population and their medical history, the Russians used the same system as in the USA: identification through smallpox vaccinations. The vaccination was done on the upper left arm. The only effective way that the local Tunguska population saw to escape being imprisoned and experimented on was to cut off their arm, thus making themselves untrackable.

In effect, there was a Western Syndicate, based in the USA and supposed to control the entire world, and a Russian conspiracy that had something the Americans didn't: Black Oil and a vaccine research program. The Russians sent their agents Marita Covarrubias and Alexander Krycek to infiltrate the western block, spies who would have to report back to the mother country. Both were able to reach key positions in prominent agencies and the Syndicate. But their loyalties were unstable: Covarrubias became a double agent for the Syndicate and Krycek a free agent selling information. In the long run, both of them served no one but themselves and the ultimate goal of resistance to the Colonists.

After the end of the Cold War, the Syndicate extended its sphere of influence to the former Soviet Union. Aware that the Russians had a source for Black Oil, they activated their contacts in Russia (American ambassadors, Russian diplomats) and found out about the Tunguska experiments. With much precaution, these contacts were able to smuggle rocks containing Black Oil from Tunguska to American soil. On a very tight committee composed in particular by C.G.B. Spender (Cigarette-Smoking Man) and the Well-Manicured Man and headed by virologist Dr. Bonita Charne-Sayre, the western vaccination program started taking shape. The experiments were conducted on elderly people in convalescence homes. By the end of 1996, they were able to prevent the coma induced by the Black Oil, but not to kill the virus.

The Russians came to know of this theft and recontacted Krycek over this matter. Krycek, with the help of former KGB agent Vassily Peskow, was able to terminate the American experiments; Dr. Charne-Sayre was killed and the smuggled rocks were destroyed.

In 1998, Krycek initiated a chain of events that led to the Syndicate acquiring the Russian vaccine; with their own previous experience and experimenting on Covarrubias they were able to improve it still. The result of world-wide human effort was an inoculation that exterminated the Black Oil from the infected human one-time only but did not provide immunity. It was notably used on FBI agent Dana Scully inside the alien environment of Base 1 at Antarctica.

The discovery of an underground deposit in Blackwood, Texas gave the Syndicate ample raw material for a vaccine research. Roush Technologies was the company responsible for the research.

Retro-engineering of alien technology not only brought advances in military aircraft but also in the field of nanotechnology, thanks to the growing knowledge in the manipulation of matter in the molecular level as of the late 1990s. From self-replicating repairing technology were developed nanorobots that could be inserted in the bloodstream and controlled by radio waves. These robots could be used to kill someone, but they also offered a very good potential to become the ultimate antibiotic. Indeed, nanorobots could designed to be able to track and destroy certain entities inside the human body: such an entity could be the Black Oil. This nanotechnology could become the much sought-for vaccine.

It was with this in mind that Conrad Strughold tried to export this technology from the USA and bring it to Tunisia, using a funding bill that would provide medical technology to Third World countries through the WHO. What became of this is unknown, as other events occurred that probably pushed these matters into oblivion.

Since 1947, human world leaders and the Syndicate had believed that the colonization would result in the human race being enslaved by the alien Colonists. The nature of the Black Oil hinted that humans would become hosts to Purity, and the Syndicate worked towards efficiently spreading the Purity virus on humans when the day would come.

But the 1998 Blackwood incident revealed that humans would not serve as a host race: they would all be exterminated! If Purity willed to do so, infection by the Black Oil could trigger a gestation of an alien entity inside the body of the host; hatching of this entity through the chest would lead the human host to his death; the alien entity would grow to become an grey alien Colonist. Mass spreading of the Black Oil would exterminate every single human infected, the sole survivors being the hybrids and a limited human resistance. The Syndicate considered this complete turnaround of events as a betrayal; the Well-Manicured Man refused collaborating any longer and sacrificed himself to help make the truth known. But at this point there was little the Syndicate could do to resist.

In 1998 also appeared on Earth the Faceless Rebels, the remaining survivors of the colonization of the race of the Shapeshifters, still actively fighting against Purity's actions in any way possible. On Earth, they saw fighting against the Syndicate and the agreement with the Colonists as a way to stall colonization and put aback Purity's plans. They sabotaged the communications routes with the abductees' implants and called for gatherings of abductees, where the abductees were relentlessly burned to death.

Purity did not stay idle and stroke back. A war had begun between Colonists and Rebels, and the Syndicate had to choose sides. The Syndicate captured the Rebel leader from his downed ship; by choosing to deliver him to the Colonists they effectively refused any kind of deal with the resisting Rebels and remained sided with their future masters. The Rebel leader was rescued by his own people.

Cassandra Spender, C.G.B.'s wife, was one of the original Syndicate family members surrendered to the Colonists in 1973. In 1999 she became the culmination of the hybridization effort, the first successful alien/human hybrid by gene therapy. The Syndicate members had to choose whether to destroy and hide this achievement or surrender her and themselves to the Colonists, a point of no return for colonization. But the Rebels chose for them; they started the burnings again and attracted unnecessary attention to Cassandra; they offered a last chance for an alliance with the Syndicate but they were met with the same rejection.

Expecting to meet the Colonists and fulfill the terms of the agreement, the Syndicate members and their families gathered in El Rico Air Force Base. The Rebels were the only ones to appear, burning them all down and putting an end to 25 years of collaboration and striking a severe blow to the colonization preparation. The Syndicate was dead!

The survivors of the Rebels' coup were few. C.G.B. Spender and Diana Fowley escaped together. Spender went on to make an attempt to turn himself into a hybrid by brain surgery with his illegitimate son Fox Mulder, but this operation failed and he became terminally ill. He lost all hope for mankind and had rather see it crumble with him than to resist until the very end. He tried to revive the project but he was stopped by Krycek.

Krycek and Covarrubias stayed true to themselves by forming a core of resistance, possibly instigating an alliance between the Russian conspiracy and the Rebels. The effect that any kind of resistance will have is open to debate; however, the Colonists have not given up on the colonization Project and have picked things up where the Syndicate left off. Colonization seems inevitable.

Half-hidden among all these materialistic events is a world of spirits. The afterlife, immaterial sentient beings, Walk-ins are all proof of these multi-layered planes of existence, if one is receptive enough to perceive them. Walk-ins are good-intentioned spirits that are able to alleviate someone from extreme suffering by taking him from the material world to the spiritual world; they are also known as guardian angels. The dead can also appear to the living and communicate with them. The intentions and the effects that all of these can have to the future course of events is only for us to see. However, the Walk-ins announce that a new age, the Age of Aquarius, will rise on December 22, 2012 AD.