After the Syndicate was more or less neutralized, the aliens had to take matters into their own hands to prepare for the colonization. The agreement forced onto them in 1973 was no longer in hand, they could go back to their original plan: the Supersoldiers.

The Supersoldiers are creations of the alien Colonists; they are humans whose DNA has been deeply modified by a version of the Black Oil virus and further compounded with iron, they are virtually indestructible, they have an iron vertebra (which is the cause for small lumps on the base of their neck) from which they can reconstruct themselves and they have an alien consciousness which prevails over their human will. The human that is to be replicated into a Supersoldier must undergo painful and very long procedures; it would seem that only people with a certain genetic profile are suitable to be replicated. Research to create a faster way to replicate and a way to replicate anybody seem to be ongoing.

Their goal is to prepar colonization. Following replication, the Supersoldiers infiltrate human society and try to attain high position of power. The first Supersoldiers may have appeared as early as 1947; the infiltration never stopped despite the agreement with the Syndicate. A second wave of Supersoldiers was created in the late 1980s-1990s. The destruction of the Syndicate Elders in 1999 effectively activated these sleeper agents, with Supersoldiers filling the power vacuum left over by the elders in their official positions. In 2000-2001 a third wave was created from the replication of what used to be abductees. By 2002 they were a very powerful and influential group infiltrated in all governmental agencies: the Treasury Department and the FBI ("Toothpick Man"), the NSA ("Shadow Man"), the intelligence community and the Mount Weather Complex (Knowle Rohrer) or the Department of Justice (Shannon McMahon) -- but they were also simple civilians in less prominent positions, fulfilling groundwork operations (Billy Miles). After the colonization they are destined to become a slave race of their masters, the Colonists.

Zeus Genetics was a fertility clinic, employing Drs. Lev and Parenti, which used its official line of business to cover for the work it did on the account of the Syndicate. Using alien genetic material, they created essentially alien babies implanted, gestated and born from human wombs. Ex-abductees left barren were used as surrogate mothers; ex-Marine Duffy Haskel infiltrated MUFON groups on the Syndicate's behalf and brought them to Zeus Genetics. The babies, stillborn, were used to provide alien tissue and genetic material for further babies and experiments on hybridization with other branches under the Syndicate.

After the Syndicate fell, Supersoldiers replace Zeus Genetics' superiors; Zeus Genetics unwittingly came under the influence of the Supersoldiers. The goal became to create a Supersoldier baby out of genetic manipulation, without the complex time consuming procedure necessary for an adult replication. This research was presented by the Supersoldiers as steps towards the creation of a perfect human being with no frailties, but it was really research to create an 'organic' version of the Supersoldier, as much alien as themselves. The Supersoldiers put an end to Zeus Genetics when another concurrent project, the Valor Victor, succeeded before them.

Similarly to Zeus Genetics, the top secret Navy research ship Valor Victor was used by the Supersoldiers to research a way to create 'organic' Supersoldiers. The Valor Victor succeeded in creating such a technique by using a modified version of the chemical additive and disinfectant to the public water supply, chloramine. The chloramine would carry a version of the Black Oil virus which would trigger a gestation inside a woman. With continuous ingestion of water throughout the fetus's and the baby's life, the virus would progressively modify the baby's genome and turn it into a Supersoldier. Ex-abductee (and not barren) women, identified through the implants in their necks, were the targets for these apparently miraculous gestations. This technique led to the creation of a whole generation of future Supersoldier babies, born in 2001. These babies exhibited telekinetic powers early on in their development. On the day of the colonization they will probably be used to eradicate any kind of human resistance thanks to their privileged position inside human societies and their apparently innocent appearance.

A specific form of the iron oxide magnetite can affect alien technology, from ships to Supersoldiers. The magnetite is believed to interact electromagnetically with the iron that is compounded in all alien technology. Magnetite is the only known way to destroy a Supersoldier. The source of this form of magnetite on Earth is mostly from crashed meteors, which makes it very rare. Magnetite may have been the reason why the Black Oil in the Tunguska meteor crash was weakened. Magnetite can also be effective in a suspended solution form that is suitable for injection. The Roswell crash revealed this weakness to the US government, however its rarity made it an unsuitable tool for resistance.

Various cosmic events such as the crash of meteorites containing Black Oil and magnetite have come to influence the biology of humans through shock mutations or prolonged exposure. A group of humans in Asia came to become immune to the Black Oil: once it would enter their body it would be killed and expelled. Thanks to a small amount of cross-breeding, the descendants of this group remained genetically pure and still exhibited similar traits. Descendants in the Tunguska region were used in the Russian conspiracy's experiments with the Black Oil and may have been the cause for the creation of the vaccine against it. Descendants in the Philippines could exhibit faculties of alien origin such as mind reading (Gibson Praise). Migration through the Bering Strait thousands of years ago brought descendants to America. It is possible that the Anasazi were immune to the alien virus; their survival in proximity with the aliens allowed for alien cultural elements (such as writing and beliefs) to be passed on to them. Because of their immunity, many of them were abducted and executed; the remainder realized the aliens feared the same form of magnetite that was present in New Mexico and retrieved in that area, only to be starved out. A group of Mexican Indians, the Huichol, still are naturally immune to the Black Oil to this day.

The aliens have specific plans for the future. Through their Ships, they have carried out the plan of the creation of mankind over millions of years and prepared colonization. The plans they have for the immediate future are as solid as what has come to pass. Their godlike powers can only be interpreted by inferior human minds in ways that only approach the truth; also, the information that is passed on to humans from the aliens and the Ships is only what the aliens choose to be. Thus, what we know of these plans should be treated with caution. Their plans have come to be known to humans as prophecies. Through various contacts over human history, parts of alien lore have survived in human cultures, notably in Northern America. The Native American tribe of the Anasazi, and the Navajo after them, use writing that is similar to the alien one. One of these prophecies is the fixed date for colonization, which marks the end date of the Mayan calendar.

Another prophecy is that a chosen one will become the leader of the colonization. However, he may be influenced by his father and follow a different path which might ultimately ruin the plans for colonization. The Colonists, and the Supersoldiers under them, work and strive for this leader to be on their side. The Anasazi only kept the human side of the prophecy in their lore, hoping that this leader will become a savior for mankind.

This important person proved to be William, the son of FBI Agents Fox Mulder and Dana Scully. Scully, left barren from previous experiments, was given her fertility back through contact with an alien Ship, which gave the child the special status of being brought into existence through the 'divine' deeds of the Ship. His subsequent conception was natural. After his conception, William was added in the chloramine program; the chloramine slowly worked his progressive conversion into a Supersoldier. This process was cut short by an injection of magnetite by Jeffrey Spender, which irrevocably eliminated traces of alien biology in him. William was given up for adoption, making his whereabouts unknown. However, his existence is still subject to the prophecy until the date of the colonization, where one of two possible outcomes will be decided.

The long-before planned date for the final alien invasion.