They're Breeding Human-Alien Hybrids
Though the U.S. government ostensibly controls Area 51, many conspiracy theorists suspect that the secret base has been co-opted by extraterrestrials, and that the little gray beings now are either sharing authority or even running the show. And why would they do that?
One suspicion is that they've set up laboratories in which they're working, possibly alongside government scientists, in an effort to breed a race of human-alien hybrids. Theorists' feverish minds offer varying explanations for this project. An article on the website Collective-evolution.com, for example, explains that the goal is to create a cadre of fifth-column agents/future leaders of the New World Order, who look exactly like the rest of us but secretly possess "the mental/psychic capabilities and social cohesion of the aliens" [source: Estep].
Others think the aliens have an even creepier purpose. The alien-human hybrids, who are under alien control (through some sort of electronic implants) are being created as a supply of organs that the extraterrestrials need to replenish their own bodies [source: Darlington].