With collaborative alien participation it seems, the government are leading the "official" colonisation project, which aims to recreate humanity utilizing the "Paper Clip" experiments.

• The conspiracy's first attempt at colonising is with the Litchfield experiments, a secret government eugenics project in the early 50's. A number of children were born with an extra 10 chromsomes, which gave them a higher IQ. However a side effect was that they were prone to psychotic behaviour and suicide. The girls were called Eve and the boys were called Adam. Eve 6 tried to clone herself to prevent any of the side effects mentioned above. When Mulder and Scully investigate the matter the project is shut down. It seems later on the conspiracy perfects cloning, with the help of the shapeshifters, and finds a use for it.

• Aliens came to Earth in 1940 and established a colony of clones based on the two original visitors. The 'Samantha' shown in 'Colony/End Game' may look nothing like the real woman and is likely, along with the 'doctor', the product of the orginal. This colony believes, and later we see the shapeshifter race does as well, that they will one day inherit the Earth but have been forced to scatter as the clones are identical. To make future clones look different they work in abortion clinics to find a way of combining human and alien DNA. However the experiments were not official and made the shapeshifter race impure, so a bounty hunter was sent to wipe out the colony. The reason the colony was mixing human and alien DNA, which is supposed to be a great sin for their race, may be because they are shapeshifter rebels and don't believe in not mixing DNA. The reason they can't shapeshift is probably because being a hybrid means you can't shapeshift.

• An official colonisation project is being led by the Cancer Man and the council of Elders. They seek to create "a new origin of species" in league with the shapeshifters. Jeremiah Smith is just one of the clones produced in the project and is referred to as a drone. He keeps care of the SEP cataloguing numbers which are stored in the Social Security computer system. The reason why the Jeremiah Smith clones can't shapeshift to avoid detection is probably because they can only shapeshift for a certain amount of time before they return to their natural form. One of the Jeremiah Smith clones thinks differentely to others of his race and is against the shapeshifters colonising Earth and rebels.

• Serial ovatypes, clones, who in this case can't speak, work in farms preparing alien foodstuffs for bees, which may be the cause of their deadly sting. It seems that clones can be bred in certain ways i.e. to speak or not. In Jeremiah Smith's case it is necessary for him to speak to perform his job.

• The clones in 'Momento Mori' are able to speak unlike their younger forms, because they are bred to speak. Mulder says they are hybrids but it is strange that the shapeshifters would want this, unless their views have now changed dramatically.

• We now may have a name for group that manages the colonisation - Roush. This was whom Kritshgau was employed by other than the DoD and we see Skinner investigating the Roush matter by going to the cloning hearings.

• Emily is another form of hybrid clone like the Crawfords seen in Momento Mori and like the Crawford clones is the product of abductee's ova.

• The government are also using elderly women from retirement homes to further the colonisation program, not just abductions. In the one retirement home that Mulder stumbles across, called the Dimsdale Retirement home, he finds that the elderly women residents were injected with hormones and that they all gave birth only a few years ago. In the same place he discovers cylinders containing live 'human' embryos floating in a green fluid, these are the result of the residents giving birth and are likely to be similar to the clones we saw floating in Momento Mori.

In summary: The government and the shapeshifters are together, carrying out the colonisation of Earth, a plan which is referred to as the "Project". The shapeshifter race believe that they will naturally assume the stewardship of the planet as the humans are forfeiting it. The conspiracy make a deal with the shapeshifters to help them in their colonisation project because then they will have more power and be a "commandant" over their own people.

Several drones are produced to help do work for the shapeshifters/conspiracy which will cause the Earth to be theirs. These drones help out on farms, cultivating bees from alien foodstuffs, these bees are killer bees and carry the disease smallpox. Others, such as the Jeremiah Smith drones, keep records of the human population on the Social Security system. These jobs will presumably have an important use when the "process" begins.