In the years leading up to the Great War, Vault-Tec initiated "Project Safehouse", producing a series of underground fallout shelters in the event that the War did indeed go nuclear. These fallout shelters, colloquially referred to as "Vaults", had a far more devious purpose than protecting the human race from nuclear annihilation. They were, in fact, secret experiments designed by the United States Government to test the effects of various factors on human subjects. Only 122 Vaults were constructed to hold one thousand occupants, nowhere near the millions that would be necessary to house the entire US population at the time, and some were not completed before the Great War broke out.
There were however, a small number of "control Vaults", in which no experiments were conducted and would act as they were advertised. Some of these control Vaults were outfitted with a G.E.C.K (Garden Of Eden Creation Kit), which could restore the surrounding environment back to it's pre-war state.
Fallout 3, shows several of these Vaults located around the Washington D. C. area. Inhabitants of Vault 87 were exposed to the Forced Evolutionary Virus (FEV), which caused rapid mutations, and was responsible for creating the East Coast breed of Super Mutants. Vault 92, claiming to be a shelter to preserve artistic talents was, in actuality, a program designed to see if white noise could be used to brainwash people into becoming super-soldiers. Vault 101, where the game begins, was designed with a "never leave" policy in mind, and to study the effects of an omnipotent dictator controlling every aspect of daily life.
In Fallout: New Vegas, Vault 3 was a control vault which was meant to open after 20 years, but the inhabitants decided to keep to Vault closed for an indefinite period of time, fearing the dangers of the outside world. However, a water leak resulted in the residents being forced to open the Vault, at which point they were immeditaely masscared by a raider gang known as the Fiends, who now use Vault 3 as their base of operations. Vault 22 was designed with the purpose of sustaining inhabitants solely on crops grown within the confines of the Vault; fungal spores, however, mutated the occupants into "Spore Carriers," a carnivorous human/plant hybrid creature. Generally speaking, most Vaults only gave the security staff access to the armory; Vault 34, however, was designed to see how the inhabitants would react if everyone within was given the opportunity to use weapons. Despite this, the Overseer feared what would happen if the populous were allowed to use the guns and limited the access to the armory. Several inhabitants left due to this disagreement, forming a tribe called the Boomers at Nellis AFB. Later on, a rebellion would occur within the Vault, during which the nuclear reactor that powered the Vault was severly damaged, leading to the remaining inhabitants becoming feral ghouls.
While most Vault Experiments ended in failure, Vault 21, built under the Las Vegas Strip, was actually a success. Vault 21 was designed with the purpose of solving all problems through gambling, and all of the candidates "selected" for entry were gambling addicts. Since the end of the Great War, it has been converted into a Casino/Resort on the New Vegas Strip, with various corridors being sealed with cement.
Fallout 4 shows more of these Vaults located around the Boston area. Vault 111's inhabitants were subjected to long-term cryogenic suspension under the pretense of being "decontaminated". The Vault staff eventually became split into two factions; those who sided with the Overseer in keeping the Vault closed (due to them receiving no All-Clear Signal following the mandatory shelter period, leading them to believe that the radiation outside had not declined enough to be survivable), and the Vault security staff who desired to leave the Vault due to dwindling supplies. This resulted in a mutiny that left the test subjects unattended, leaving them frozen for over 200 years.
Vault 95 was populated solely by drug addicts. Five years after the vault was sealed, a hidden stash of drugs was unlocked. Within a few days, all of the vault residents but one fell back into addiction or killed each other. By the time of the game, Vault 95 is inhabited by Gunners, and the Sole Survivor travels there to cure their companion Cait of her chem addictions.
Vault 81 was initially built for the purpose of creating a single cure for all diseases. Unlike the other vaults however, Vault 81's residents were saved from the hideous experiments of the Vault-Tec scientists thanks to the original overseer's sudden change of heart by having the equipment disabled which would have otherwise allowed the scientists to expose the residents to diseases.
Vault 75 was built underneath Malden Middle School, and was advertised as a shelter for the school's students and their families. However, upon entering the Vault, the parents were separated from the children and executed by the security staff. Vault 75's purpose was to enhance the gene pool of the residents to create stronger and more intelligent subjects. To achieve this goal, the children were tested both mentally and physically to the point of borderline torture, and were told that upon 'graduation' when they turned eighteen, they would be released to help the people of 'Uptopland' (a nickname the residents gave to wasteland). Those with exceptional intelligence and physical health were harvested for there genes, more intelligent subjects who displayed obedience were recruited to the Vault's science team, and those who did not meet expectations were killed following their graduation ceremony. By the time of the game, Vault 75 has been emptied and is now used as a stronghold by the Gunners, like Vault 95.
Fallout 76 introduced the control Vault, Vault 76, located in Appalachia in West Virginia. As per its status as a control Vault, Vault 76 was set to open approximately 20-25 years after the Great War, completed and opened in celebration of the United States' tricentennial in 2076. Alongside Vault 76, at least four other Vaults were in Appalachia. Vault 79 was built to house the United States' gold bullion reserve from Fort Knox in the event of nuclear war. Vault 63, Vault 94, and Vault 96 remained sealed and inaccessible, though when a revolt occurred in Vault 94 by the wastelanders who had been welcomed into the Vault by the peaceful Vault residents, the wastelanders shot the G.E.C.K. system and caused it to suffer a nuclear meltdown and cause vast mutations to the area around the Vault, transforming it into The Mire. Anyone affected by the radiation released by the meltdown was severely mutated by it, if not turned into mindless feral ghouls because of it.
However, Vault 76 remained peaceful until Reclamation Day, when the Vault reopened to allow the residents to recolonize the Appalachian Wasteland, but was designed to shut down once the last of the residents had vacated the Vault. Vault-Tec had given the overseer of Vault 76 special orders for her and her residents: Three of the United States' surviving, and still active, nuclear I.C.B.M. missile silos were located in Appalachia: Site Alpha, Site Bravo, and Site Charlie. Vault-Tec wanted the silos secured, even if it meant going against surviving members of the United States Armed Forces that guarded the silos, including the USAF missileers in charge of the launching the nukes as with contact having been lost with the Enclave oil platform, Vault-Tec felt it was their duty to secure the nukes themselves as the successors to the United States' federal government. However, the overseer was unable to gain access to the silos due to being unable to make contact with and meet MODUS, the Enclave A.I. that was in charge of the Whitespring Bunker and could provide the necessary means to gain access to the silos, along with the other parts of the Appalachian Automated Launch System with acquiring a nuclear keycard from the Strategic Air Command cargobots that carried them, and the nuclear launch codes carried by former U.S. Armed Forces personnel that had succumbed to the radiation and become feral ghouls, or become members of the Scorched, a potentially genocidal plague that had affected Appalachia in the years after the Great War as a result of the scorchbeasts, man-made monstrosities that had been unleashed on Appalachia as a means for successor President Eckhart to gain access to the nukes to finish off the People's Republic of China. As a result, the overseer asked her residents to use the nukes to take out the scorchbeasts before they and their queen could spread beyond Appalachia, but it is possible that the residents wound up turning the nukes on Appalachia itself instead of taking out the fissure sites where the scorchbeasts were making their way to the surface to unleash their fury on Appalachia.
Still, Vault-Tec's decision with Vault 76 proved to be a valuable asset as rumors of Vault 79's contents caused many a person to return to Appalachia to aid the Vault 76 residents in rebuilding the area, and possibly gain access to the gold bullion housed within Vault 79 itself, so Vault-Tec may have had some good intentions, despite its villainous intentions for most of their Vaults.