Stable 99 was a Fallout shelter, designed to save the lives of ponies and allow future generations to flourish.
Stable 99 was designed as a control stable, but was given a unique recycling system that would convert organic matter into edible food, rather than its own apple orchard where the ponies could grow their own food. The stable gradually evolved into the strict system of breeding and control, the same goes for their recycling of dead bodies, rather than burning them.
The Stable originally was supposed to have a social experiment, but Scootaloo instead left a recording, ordering the Overmare to make sure the ponies survived. The stable was also were the megaspell EC-1101 ended up becoming trapped in the stable's systems after external connections to the rest of the Stable-Tec network were damaged.
Over time the roles of stable residents became strictly hereditary, with a resident's child taking over her role once their parent died. The population was also kept stable through the use of sterility implants. The role of the Overmare became particularly sacred over time, with communal music and propaganda encouraging loyalty to both the Overmare and the good of the Stable.
One Hundred and Sixty Years Later
The stallion population of the stable were upset with their living conditions and their involvement in raising the stable's foals. It was only when the hereditary found a way to work in favor of the stallions: when the Overmare of the time gave birth to a colt instead of a filly. Though the details are unclear as to what exactly transpired, the revolt was crushed and the stallions were segregated to their own portion of the stable and closely monitored. It is around this time that the breeding queue system was introduced, whereby males are housed in medical and released solely for the purposes of breeding and 'recreation'. The population of the stable remained at 500 mares and 40 stallions; despite (and possibly because of) the strict breeding controls and large female population, relationships between mares tend to be common and casual.
The next Stable Overmare was noted as being extremely paranoid and power hungry. Blackjack was the daughter of the Stable's security chief and was to take over her mother's position when she was older. Blackjack tracked down P-21 who was hiding because he was scheduled to be killed/euthanised. Blackjack learns of the Overmare's corruption and collaboration with a group of ponies outside the Stable (supposedly Stable-Tec), though things took a turn for the worse when a massive cyberpony named Deus gained access to the stable and began slaughtering the residents in his search for EC-1101. After ordering the Midnight to get everyone down to the lower levels and forming a plan with her mother, Blackjack lures Deus and the Raiders he was leading out of the stable after transferring EC-1101 it to her Pipbuck as bait.
Unfortunately for the Stable dwellers, the raiders that Deus was leading were infected with the Raider Disease. The disease infected a portion of the stable dwellers who began killing and devouring their fellow ponies or converting them with infected bites; they would later journey out of the Stable at the command of the now psychotic Overmare and capture wastelanders to consume and bolster their numbers. Blackjack returns to Stable 99 when she hears the surrounding area is a hub of heavy raider activity. Once Blackjack and her friends reach Stable 99, they fight their way through the crazed ponies on the upper levels and find the sane and uninfected survivors in the lower levels, lead by Rivets.
Blackjack helps lead a counterattack against the infected stable dwellers, eventually killing the Overmare leading them and then Daisy who had poised herself to take over the raiders. After wiping out any surviving cannibal ponies, Blackjack in her exhaustion tells the stable dwellers to burn the corpses. Blackjack and P-21 try to inspire positive change in how the stable is managed, but the ponies don't want to listen and wish to go back to the way things were (including many of the males kept for "recreation", much to P-21's horror). After receiving a petition from over 100 stable residents to depart, Blackjack prepares to leave but upon visiting the lower levels of the stable, comes across Scotch Tape who is performing maintenance on the recycling system. The machine bursts and Blackjack - to her horror and disgust - sees that the stable dwellers have not heeded her warnings, but actually put the infected bodies into the recycling system, contaminating it.
Blackjack orders Scotch Tape up to the stable door, after confirming she hasn't ingested any infected food and then heads up herself after a heated exchange with a now crazed Rivets. Blackjack, starting to see early signs of the raider disease in the dwellers, resolves to keep Hoofington safe from an outbreak; she threw her pipbuck through stable door after her friends and sealed it, before activating a talisman that fills the stable with chlorine gas, rapidly killing all of the inhabitants. Blackjack intended to die with them due to the shame of what she was forced to do, however is rescued from Chlorine poisoning by Lacunae working under the directive of the Goddess.
After encountering Paladin Crumpets at the Fluttershy Medical Clinic, the Stable's location is given to the newly formed, Hoofington, Applejack's Rangers by Blackjack as a potential base of operations. The stable was partially looted by scavengers, before Blackjack warned the traders who hired them about the Rangers who were moving in.
It was later revealed that some uncontaminated stable ponies survived in an isolated portion of the Stable (other secure areas contained pockets of contaminated residents, however these proved no match for the Rangers). They were rescued and recruited by the Applejack's Rangers as they had both the expertise and subterranean dwelling ethic necessary to work the Stable's systems. Despite being staffed by both the Rangers and survivors however, the population was too few to adequately maintain the Stable's numerous systems, leading to fears the remaining inhabitants would have to evacuate with the Rangers to Trottingham.
Following the discovery of the classified Stable 96 in Shadowbolt Tower however, and the subsequent evacuation, the population is greatly boosted by the migrant Stable Dwellers. Currently the population of Stable 99 stands at 216 unicorns, 92 earth ponies and 60 pegasi from Stable 96, 13 original survivors from Stable 99, all lead by Overmare Fargazer, and a garrison of Steel Rangers lead by Star Paladin Stronghoof.
Notable Residents of Stable 99
Blackjack - Blackjack is the protagonist of Project Horizons and was born into stable 99 and was to be the next head of security.
P-21 - The latest earth pony breeder to gain the designation of P-21, he was to be euthanised prior to escaping Stable 99 with Blackjack.
Scotch Tape - Scotch Tape was in training to become the next head of maintenance in Stable 99. She was being trained by her mother, before she was orphaned by Duct Tape's death. She leaves Stable 99 with Blackjack and her friends.
Midnight - An attractive mare who Blackjack was infatuated with, prior to leaving Stable 99.
Duct Tape - Mother of Scotch Tape. She was infatuated with P-21 whom she hoped to escape Stable 99 with and start a family. She was killed when a rigged terminal exploded.
Card Trick - The first chief security mare of Stable 99 and Blackjack's ancestor. Also the original owner of Vigilance, which is passed down from mother to daughter as a form of 'rite of passage.'
Gin Rummy - Blackjack's mother and the head of stable security, prior to Blackjack leaving the stable.
Rivets - Head of Stable 99 maintenance and leader of the attempted insurrection against the Overmare.
Daisey - A massive and overzealous security mare on the same shift as Blackjack.
Marmalade - A dimwitted, yet surprisingly friendly security mare on the same shift as Blackjack who follows Daisey around.
Textbook - Blackjack's teacher during her time as a filly, who believes her to be the worst teacher in the whole of Equestria.
U-21 (previous) - P-21's lover, a Unicorn breeder that had reached his retirement while the earth pony was still P-16.
U-21 (current) - A Unicorn breeder that was recently scheduled for retirement, yet was spared by the Overmare to covertly investigate the surface. Encountered and sided with Deus in his assault on Stable 99 and helped him in hunting down Blackjack and P-21.