Rebels: "There also exists a faction of aliens who actively oppose Colonization. They are the same species as the Alien Bounty Hunter(s), free from the effects of black oil infection. The Rebels are distinguished by their grotesque appearance: the orifices on their face are morphed shut to avoid absorption of the parasitic black oil."
"Colonization has apparently begun in the Rebels' home environment, but members of this species are spared gestation to become Bounty Hunters for the Colonists' ongoing conquest efforts. Although enemies of the Colonists, the Rebels can also be hostile to humanity; they carry prod-like weapons that can quickly incinerate a human and do not hesitate to use them."
"They burn abductees with chips in their necks at abduction sites in attempts to prevent colonization from proceeding. The Rebels have a vested interest in keeping the Colonists from finding out that a successful hybrid has been created. While the Rebels had an opportunity to destroy the hybrid, Cassandra Spender, they choose to let her survive in the hope that the Syndicate will join them in fighting the Colonists."
"If they refuse, Cassandra can be used to expose the truth and the conspiracy. The Rebels go so far as to infiltrate the Syndicate and bring up the possibility of fighting the Colonists. However, the Syndicate decides that fighting the Colonists would be futile. At this point, a fully working vaccine has not been created, and it is therefore decided that the best thing for the Syndicate to do is to comply with the original deal and turn over the hybrid to the Colonists in the hope that they are spared the resulting takeover."
"Before this can be done, however, the Rebels kill all but a few members of the Syndicate in addition to Cassandra, the only living successful alien-human hybrid, before the Syndicate is able to send a signal to the Colonists. Without a successful hybrid, the timetable for the Colonist invasion will not be advanced and the date set for colonization remains December 22, 2012."
Alien-human hybrids: "Early attempts to create alien-human hybrids were pioneered by German and Japanese scientists shortly after World War II, and for some time during the Cold War. However, these often met with failure, and the Syndicate started to rely more on their own scientists."
(See "Nazi Space Program")
"According to the Alien Bounty Hunter, in the 1950s, Soviet geneticists found a unique genetic anomaly within identical twins. The Colonists and Syndicate scientists used this to eventually develop human clones with alien elements and partial hybrids, but they were still ultimately inferior."
"Hybrids of this type include Samantha Mulder, Kurt Crawford, the Gregors, Ernest Calderon, and Dr. William Secare. Child and adult versions of Samantha and Kurt are also seen. These clones have the same caustic greenish blood of the aliens, have greater muscular strength and higher physical endurance levels than most normal humans, and can breathe underwater. In addition to their intended use by the alien colonists, the Syndicate is occasionally seen using these clones to perform various tasks, such as research and physical labor."
"The pinnacle of the project is Cassandra Spender (Veronica Cartwright), mother of Jeffrey Spender (Chris Owens) and ex-wife of The Smoking Man. Cassandra is a hybrid created through a process other than cloning, and worked on by both the Syndicate and the aliens themselves, although the exact methods used to transform her are never fully revealed. The experiment presumably began when she, along with other family members of the Syndicate, were turned over to the colonists in 1973."
"For years, Cassandra was under the mistaken impression that she was to be an emissary of the aliens to spread a higher spiritual understanding to humanity, but after her final abduction in the late 1990s she comes to realize the truth. She is killed, along with most of the Syndicate, by the alien rebels."
"After being exposed to an alien artifact, Mulder slipped into a coma, although he was imbued with telepathic abilities. In order to find a cure for her partner, Dana Scully (Gillian Anderson) discovered a book containing Native American beliefs and practices; the books described how one man would be able to hold off the forces of the apocalypse and become humanity's savior."
"Meanwhile, The Smoking Man took Mulder and prepped to have his genetic material—the same material that allowed Mulder to become telepathic—implanted into him. He believed that Mulder had, in effect, become a perfect alien-human hybrid and that by taking his genetic material, he would be able to continue "The Project" and survive the coming alien onslaught."
Super Soldier: "With nearly every Syndicate member dead, the Colonists began to clear up any evidence of alien life and began to create human replacements called "Super Soldiers," on which the Colonists had been working covertly as an alternative slave race should the hybridization experiments be unsuccessful."
"To create Super Soldiers, the Colonists infect humans with a new strain of their virus, which slowly destroys and then rebuilds the body of the host. This process seems to involve a lengthy surgical procedure on abductees as opposed to simple infection (as with the black oil)."
"As they have normal red blood and can replace individuals within powerful positions, they provide an ideal way for the Colonists to infiltrate humanity to ensure that the plans for colonization are uninterrupted. They are identifiable however by small spiny protrusions on the backs of their necks or by detailed analysis of a blood sample which shows their DNA exists as a complex with iron."
"Although they cannot shapeshift, Super Soldiers are practically unstoppable. They can survive being crushed by a garbage compactor, decapitation, and can rip through steel with their bare hands. The only known way to kill them takes advantage of their metallic biochemistry: their bodies are torn apart by the magnetic fields present near large deposits of magnetite ore."
"The Super Soldiers quietly fill the positions of power previously occupied by Syndicate members and rarely use human conspirators. By the end of season 9 they virtually replaced the Syndicate and were successful in chasing Mulder and Scully out of the FBI so that they can no longer investigate the X-Files and interfere with their plans. As of their last appearance, they were preparing for the final invasion in 2012."