A bit of a setting dump about a section of Post-War Equestria; obviously there are a lot of brains in it....

Big MT

This Equestrian area was dedicated to top-secret scientific and magical research before the world ended. Now a bombed-out crater, this otherwise isolated area is only accessible by teleportation or underground river, as pylons among the crater’s top make it impossible to enter via flight or observe inside.

There are several societies in the crater.

The first is the Stable. Originally designed to be a refuge for MT staff in event of apocalypse, it ended up being something quite different. Upon heading inside, everyone, from the oldest mare to the smallest filly had their brains scooped out and put in jars or robobrains, while their old bodies were either put in cryostasis or implanted with Tesla coils to become obedient servants.

The brains were reprogrammed to loyally serve as organic computers for the research there, but time not only deteriorated their programming but also allowed the brains opportunity to get around it. Operating under the logic that their brains would function much more efficiently if they engaged in the activities of a healthy pony society, they proceeded to gradually start their own society in the Stable. They reimplanted themselves into either their former bodies or the bodies of others on occasion, and living life, albeit with interchangeable brains.

Their society is revolved around brains- brain massages, brain reprogramming, and brain wiping are quite common. Upon gaining their cutie marks (or the relevant ages for other species) ponies and other sentient creatures have their brains removed, reprogrammed with CODE to tie their identity to their brain and not their body- then put in their very own braindome, choosing from a variety of bodies to occupy afterwards. They frequently swap bodies as well- a yak today is a pegasus tomorrow then a griffon. A body is just a piece of clothing for the brain. Those who have non-robotic bodies in the Stable wear white and grey jumpsuits.

They regularly wipe and reprogram themselves, and some brains are Pre-War! They don’t mind being disembodied and isolated for large periods of time, and some wait contentedly in jars for the day they are needed, sometimes years without sensory input. Which is useful, because there are literally thousands of brains without robot or organic bodies, sitting on shelves collecting dust.

Nearly every computer system in the Stable has an organic brain at its core. They don’t terribly mind their minds becoming the core of a minor subsystem and performing minor, almost insignificant tasks- after all, it’s what they’re programmed to feel pride at. The brain is, after all, the best computer there is.

The second is an unnamed Lobotomite village. They believe that the brain is a hindrance to true enlightenment and remove them in order to achieve a perfect state. Granted, most of them have Tesla coils in their heads so they can function without a brain- but they deliberately keep them on the lowest setting and turn them off when not working.

They are led by a mad dragon’s brain from Pre-War, who commands them telepathically to do his bidding. His body, robotic brain in head, guards the location of his mind, a hidden cavern just below the village...

The third is the Diamond Cyberdog warrens. Experimented upon to become the perfect soldier, the Cyberdogs had their brains removed and replaced with robot processors-then an organic brain was placed in their heads to be subordinate to said processor. This would create an intelligent and completely obedient super soldier, whose brain could be discarded and replaced if it got damaged.

To this end, the organic brains in their heads were predominantly pony, because they were considered to be of superior quality. Following the war, they continued to reproduce and thrive- stealing the brains of whoever entered the MT and using their bodies as slaves.

The fourth is the Mutant Lair. Experiments whose brains had been removed were dumped into the IMP (Equestria’s FEV); the new alicorns growing new, memoryless brains as a result of the experiments. Eventually, the alicorns were left with a dilemma- there were a lot of brains left over after their debraining spree. So, they did the next thing that came to mind- they dunked the disembodied brains by themselves, resulting in Floaters, or they fused the brains with animals, resulting in Chimeras or Mutant Hounds. Because they can regenerate from near anything, they frequently play with their brains, casually squishing and squashing them around without caring whether it gets damaged or not.

The fifth are the Brainminders. Formerly a group of griffon mercenaries, their brains were removed as they entered the Big MT and they were turned loose, mindless and barely functional. However, that all changed when they stumbled (literally!) upon a brain storage facility. The automated surgery systems detected their brainless state, giving them the Pre-War specimens and implanting them into the griffons’ heads.

Now the griffons have a new purpose- protecting the collected knowledge of the Old World and the minds that hold said knowledge. Their brains are removed at birth, and they grow up without the ability to think, their heads filled with nothing but silence- but they are able to function despite this. But when they come of age, they experience life with a brain for the first time- the joys of thought, as they give their ancient brains the chance to live again.

The sixth is the MT headquarters. The former heads of the MT were once Equestria’s most brilliant minds, before they were sucked out and put in jars post-war. Driven insane by the effects of not being reprogrammed to exist as brains in jars, they wish to gain access to the outside world to have more brains and bodies to experiment on... though they actually are nice when you get to know them.

They are served by a group of orange-winged Changelings, who are given authority over their experiments and love in the form of “brain food”- the leftover brains from the experiments the heads of the MT conduct. They also are known to hock their changeling slime into the empty heads of the victims of brain theft, turning them into the changelings’ slaves.

The seventh is the Draconequus Aphreno... though he stalks the plains, he is still a prominent force. Caravans are known to go missing in the night, reappearing without their brains, for he swallows them whole and keeps them alive, thinking, in his extradimensional stomach to prevent the tech of the MT from getting out. His most fervent wish is to acquire the brains of the MT in order to gain access to the technologies they’ve been thinking up...