Little Green Men
Based around the Shyamalan twist at the end of Annie Jacobsen's purportedly non-fiction Area 51 book.
Tales of aliens abound in the Wasteland. At the campfires of road side rest stops, one can hear old men regaling caravaneers with lurid tales of abduction and probing by things from beyond the stars. The old-timers in Dayglow mumble about the things they saw in the ancient ruins to the west, when they were still ripe for the picking: bulbous heads and empty eyes warped into shapes stranger still by the glass domes that contained them. Glinting saucers crashed in the desert sands, entire herds of brahmin dissected, strange symbols in fields of maize. What are we to make of these signs and portents? Mere myth?
Not so. In the days before the Atomic Holocaust, the government had a lot of money. More money than they knew what to do with, really. They were very free with how this money was distributed, throwing it at anyone and everyone who promised potentially war-winning results. And in the halls of vast bureaucracies staffed by nincompoops and neptoism hires, it was very easy for some of the more retarded plans to slip through the cracks.
The concept behind Little Green Men was simple. Cause a mass panic and undermine morale among the Chinese by faking an alien invasion, on the model of the Orson Wells
War of the Worlds panic. First state of the art, albeit highly impractical, saucer-type aircraft were requistioned. Next, some of the most advanced (but again, highly impractical) energy weapons. All of this would be covered in strange symbols and made with strange unergonomic designs that only make sense for beings not of this world. Finally, you get dozens of these things past Chinese air defenses, wreak some havoc in backwater towns and villages, and strike fear into the hearts of the Chinese people. The only ingredient missing was the aliens.
Children from some of the less fortunate corners of American society were to be drafted, given a chance to serve their country and make something of themselves - or rather, have the government make them into something else.
These children would undergo a number of horrific procedures to make them fit the role. An induced form of harlequin icthyosis was deployed to give them a horrific, reptilian appearance with scaled skin. Their eyes were widened and pulled back, and their color made black. Their head would be bound to increase capacity and elongate shape. Small amounts of lead would be injected subdermally to give some measure of protection in the highly irradiated cabins of their saucers, along with genetic modifications. Their growth would be severely retarded, preventing them from reaching full maturity.
Perhaps more important were the psychologicla and neurological modifications. Though their brain capacity was enlarged and a cocktail of chemicals and genetic therapies would increase the growth of their brain, it was specifically targeted towards sections focused on analytical thinking and memory rather than creativity or individuality. They would be psychologically conditioned in a bizarre manner: they were totally loyal to their human handlers, utterly devoted to their mission with little regard for themselves. They were made to memorize formulae and knowledge far beyond what was necessary to give the outward appearance of super-human intelligence, despite the fact that they had no ability to do anything other than what they were trained or had memorized. They were given a totally artificial language and culture, completely divorced from anything on earth, to complete the illusion of an alien race.
Thousands of these abominations were created in forgotten sections of science labs across the country - WestTek, Groom Lake, Sierra Army Depot, Dulce Base, others of their ilk. While they were waiting for full approval of their mission, science staff found that they were useful lab assistants due to their devotion and their ability to memorize complex but ultimately monotonous tasks.
When word finally reached someone capable of making rational decisions that they had bred an army of inhuman freaks for some harebrained scheme, he said "What the fuck?" The plan was shitcanned, and all living Little Green Men were ordered to Dulce Base, awaiting extermination. The year was 2077...
After the War, their human captors extinct, the Little Green Men have developed a strange culture. Without human directions, their inbuilt instincts and memorized plots have gotten their wires a little crossed. They are now enacting their grand plan, the big mission. They wreak havoc across the American Southwest, and perhaps beyond. Ships randomly attack travelers and towns with their exotic energy weapons. Abductions and dissections are an extrapolation of their lab-assistant habits, diligently doing and logging scientific studies with no direction or purpose other than gathering data, a sadistic exercise detached from any illusion of progress. They will occasionally crash their saucers on purpose, intending to be found to strike terror into the hearts of the Reds, though it helps that they're not especially dexterous or skilled at literally anything they do.
Their lives are centered around the Mother Ship, Dulce Base. Dulce Base is run by an AI that centrally directs and organizes the Little Green Men on the basis of its remaining and scrambled instructions. The most important role of the AI is managing reproduction, growing new Little Green Men in vats from the biological material of its population, as well as the occasional hapless Wastelander, conducting all the needed operations and psycological operations. Increasingly important is sending the saucers out on more structured missions - gathering supplies and scraps from other military facilities as its own structures and equipment begins to break down.