Littlepip's first glimpse of the Crapsaccharine World she lives in causes her to collapse and have a panic attack. And then we are shown the first sight of the decimated Equestria is Sweet Apple Acres; indicating that Nothing Is the Same Anymore.
The megaspells that wiped out much of Equestria at the end of the war irradiated the land. Not only does Littlepip have to face the horrors of the wasteland but remember she is being exposed to various levels of radiation most of the time.
The very thought that characters of My Little Pony participated in a violent, bloody war that involved religious/racial annihilation, an assassination attempt on Princess Celestia, the mass murder of an entire school, the Mane Six forming ministries with questionable motives and practices, and the war ending with nuclear holocaust.
And the fact that it's written so in-character that it seems quite possible.
The Nuclear Nasty byproducts of the radiation and Taint ( actually the Impelled Metamorphosis Potion created by Twilight Sparkle to turn ponies into alicorns.) While Taint does have its quirks, such as being able to regrow lost limbs, its penalties are more severe. Taint has created such beasts as bloatsprites, bloodwing bats, balefire phoenixes, etc.
The alicorns are one of the major threats in the wasteland, standing in for the Super Mutants from Fallout 3. They are all part of a Hive Mind commanded by the Goddess, whose goal is to assimilate all creatures under her control. The Goddess herself was created accidentally from Twilight's attempt to artifically create alicorns during the war. She, or at least at the centre of her conscience is Trixie, who was to be the first test subject of the experiments.
The transformation process used by the Goddess is not actually seen but it at least involves being dragged into a vat of chemicals by telekinetic tentacles. Fallout: Equestria - Project Horizons took the liberty of filling in the blanks, revealing a pony's body is melted down and then reshaped into an alicorn while the Goddess strips the mind to suit her needs.
A haunting radio message from a mother who lost most of her family to raiders, and then her surviving son ate irradiated fruit and became close to death. Then the message repeats. Who knows how long ago the message was actually recorded.
Ponyville has become a Wretched Hive for raiders, with the Carousel Boutique empty and abandoned, and Twilight's library turned into a horrific den and is decorated with the corpses of dead ponies and animals. One poor mare gets a Crucified Hero Shot, nailed to a bookcase by railroad spikes.
The Ironshod Firearms factory is guarded by killer robots, powered by brains, and shoot anything that moves. And all the while spewing out gestures of friendship: "Don't run! We just want to be friends!"
"PINKIE PIE IS WATCHING YOU FOREVER!"
Like the Vaults in the Fallout games, the Stables are hellish in their own ways. Unlike the Vaults, the Stables were actually designed to protect ponies, but Scootaloo designed most of them to have social experiments that would mould communities that would not repeat the mistakes of the past. Unfortunately, most Stables failed in some capacity:
Stable 1, 2 and 3 all did quite well, though Scootaloo designed the first to never open until all of its original occupants (the Princesses and Mane Six) died as a Take That! for what they had done to Equestria; Stable 2 was never meant to open; and Stable 3 lasted a century before Pink Cloud infiltrated it.
Stable 24's started out normal aside from having an Overstallion and a culture leaning more towards masculinity. Until a filly used magic to accidentally fuse several animals together to create the chimera species. Within a matter of days, the chimera swept through the Stable, paralyzing everyone and then injecting their eggs into the victims. The baby chimera then crawled their way out of the bodies. Littlepip and Calamity investigate the Stable and have to blow it up, wiping out the chimeras.
Then, there is Stable 29. It lacked an Overmare but was instead monitored by a Crusader Mainframe supercomputer. Unfortunately, A.I. is a Crapshoot. When the Stable's water talisman is damaged and cannot be fixed, the Crusader Mainframe followed protocol and "preserved pony life", by systematically killing all of the residents to balance out the amount of water. The Stable lasted three months, with a last hurrah in the form of a party hosted by Vinyl Scratch. Among the victims was a whole classroom of children who are gassed to death, two ponies are burnt to death by a cleaning robot, a father and son die in an elevator crash, and the final residents all dying in the Stable's atrium, with a noticeboard marked with the blood-written message "STOP KILLING US!"
Stable 101, Red Eye's home, was turned into a mass laboratory to replicate the alicorn transformation process, with all of the residents poisoned for Red Eye to begin his goal to become Equestria's new god.
Silver Bell's terrible circumstances. Her parents were murdered before her eyes by raiders, and then her older sister Memory left to find help, only to never come back. In her despair, Silver Bell became a Stepford Smiler and decided to act like Pinkie Pie to deny her own survivor's guilt, dying her coat and mane pink and chopping off her own horn, renaming herself "Pinkie Bell". Oh, and there is a balefire bomb in the silo that is still armed.
Diamond Tiara's suicide. Trapped in the Shattered Hoof Rehabilitation Clinic with an army of cannibalistic inmates, Diamond went mad and slashed her arms to avoid being eaten.
Mr. Topaz's death involves Littlepip dropping grenades down his throat, and a third of his body is blown away. He dies instantly.
The treacherous Four Stars transportation company who were zebra sympathisers. They were willing to murder thousands of innocent ponies in Manehattan to save their own skins by hiding in a Stable hidden under their company building. All they got for their troubles was a Stable full of feral zebra ghouls.
The Ministry of Morale is basically Nineteen Eighty-Four's Ministries all rolled into one, with a drugged up Pinkie at the helm. It monitored and spied on every Equestrian citizen to look for sympathisers, traitors, naysayers, and anyone who was breaking the country's morale. Most were taken for interrogation and would have their memories examined and removed so they could be "happy".
The hallway of posters Littlepip and Velvet encounter in the MoM building, each with a huge picture Pinkie, staring and watching forever.
Pinkie's death is never seen, but it is implied she was killed by the Manehattan balefire bomb and all Littlepip finds is her skeleton.
The undead Mad Scientist who kidnapped the population of Gutterville to use them as guinea pigs in his attempt to find a cure for Taint. Those he tested it on died, and those who survived live long enough for their bodies to be twisted into horrible shapes.
While Tenpony Tower is perhaps the wasteland's most civilized place, its laws are very punishing, with theft meaning immediate execution.
The revelation that Fluttershy of all people was inadvertantly responsible for the megaspell holocaust of Equestria.
Hellhounds are considered the most dangerous creatures in the wasteland and prove it with their great strength, claws, and ability to use weapons. They are used as angry guard dogs by Red Eye and the Enclave using mind control helmets.
Fillydelphia. Just Fillydelphia. Based on the Pitt from Fallout 3, Fillydelphia was the industrial capital of Equestria during wartime. It has become Red Eye’s domain and is used for mass production via slave labour. The city is surrounded by an impenetrable metal wall which is guarded by griffins around the clock and anyone who tries to escape is immediately shot and dragged back to work.
The Fillydelphia FunFarm built by Pinkie has become the slaves’ quarters, with the park’s central giant barn turned into a massive factory overseen by Red Eye. The park’s Alpha Omega Hotel is used as a home for colts and fillies, only they are being brainwashed by Red Eye’s charisma and words, and taught how to use weaponry. And then there is the Pit, an enormous gladiator pit where ponies and other creatures fight in Gladiator Games to the death, much to the glee of the bloodthirsty audience, which mostly consists of slaves. Their glee could be justified since this is the only enjoyment they get in their miserable lives.
Xenith's life in Fillydelphia has been horrific. Beaten, abused and raped, Xenith has survived by sheer will and pretending to be a mute to avoid having her tongue cut out.
Angel Bunny is depicted as a Killer Rabbit, nicknamed "Doombunny" by Xenith's tribe, and was known as a deadly warrior on the battlefield.
Apple Bloom dies of radiation poisoning minutes after the balefire bombing of Fillydelphia. She might have survived if the door for Stable 0 had been put on.
The Littlehorn Massacre was the darkest day of the war. Due to misunderstandings between the school and a passing convoy of zebras, the zebras were killed, prompting an assassin to sneak into the school and unleash the Pink Cloud, killing everyone in the school.
Chapter 28 involves Littlepip's group returning to Stable 2 to wage war on the invading Steel Rangers. It is a long, drawn out battle that drags Littlepip through her former home and seeing many familiar faces murdered in cold blood. The biggest casualties include the welcoming committee sent to greet the Steel Rangers, and a party of fillies who had just gained their Cutie Mark.
Twilight Sparkle's death is terrifying. She is trapped in an inescapable room for three days, going mad from dehydration and thinking she is seeing hallucinations of Trixie. It actually is Trixie, who has become the Goddess, and intends on making Twilight immortal. She then uses telekinetic tentacles to grab Twilight and drag her kicking and screaming into a vat of IMP.
The fleshyhospital horrors Littlepip and Xenith encounter, based on the Centaurs from Fallout 3. They are horrible masses of flesh with tentacles for tongues and sunken eyes. They can paralyze victims using the Stare, then rape and impregnate them. Their offspring then force their way out of the body and control it. The original victim, Peachy Pie, was turned into a monster two days after exposure to Taint. She had to be dissected alive by her best friend Sunny Days to put her out of her misery since the monster she became was immune to lethal injections. This ended up being a cautionary tale for Twilight ( and the Goddess) to carefully reconfigure the IMP.
The Black Book is a zebra-written spellbook that allows its reader/owner to perform Black Magic like necromancy and creating soul jars. It is actually a Soul Jar for its owner, an insane zebra alchemist who whispers to the book's readers, manipulating them into learning and performing the evil magic within.
Arbu – “friendliest town in the wasteland” – or really a town made up of cannibals, who kill and eat all those who die in their town and those who eat their first hearts are marked as a member of the town and allowed to vote. The only one who knows the truth and tries to warn outsiders is a crazed old stallion, Grandpa Rattle, who is often kept locked up. Littlepip discovers the truth and goes on a full-scale rampage, executing everyone who has the town mark, aside from young children and Grandpa Rattle.
The Pink Cloud is perhaps the most nightmarish element of the wasteland. Appearing as a pink-coloured mist, it is actually necromancy magic that acts as a Deadly Gas, sucking the lifeforce out of everything it consumes. Those who are unlucky to be caught in it will likely die in minutes, their bodies fusing with whatever items they are touching, and their bones dyed pink. Those who survive it become Canterlot ghouls like Steelhooves and Star Sparkle, but are permanently fused to whatever item they are touching. Known victims are Twilight's mother, Princess Luna, Lyra Heartstrings, and Rarity.
An undead filly has been mutated by the cloud so much that her Cutie Mark is the Pink Cloud.
The skeleton in Fluttershy's office hanging from the window. Just another nameless victim of the Pink Cloud. Nope. This is actually Rarity's corpse. The unicorn sacrificed herself to save Fluttershy and Angel, sticking her forehoof through a hole in a magically regenerating window to prevent the Pink Cloud from entering. She then used the last of her energy to teleport Fluttershy to safety, then recorded a memory orb message for Twilight using Angel as a host.
Canterlot's final fate. Princess Celestia and Luna created a forcefield to keep out the balefire bombs, only for zebra agents to have installed the Pink Cloud inside Canterlot's treasury dragon. The residents of Canterlot were in an inescapable death trap.
The Canterlot Ministry of Peace hub was built into a grove of magically-grown trees. Thanks to the Pink Cloud, it looks like a Haunted House.
Rarity used the Black Book to split her soul into forty-three pieces and placed forty-two pieces in statuettes of her friends. The procedure used to do it is described as redefining torture.
Chapter 39 is used filled with traumatic events. Steelhooves is unceremoniously killed by a Hellhound, the Grand Pegasus Enclave descend from the clouds to "save" it via Operation Cauterize. They then proceed to blast Canterlot off the face of the earth, killing all the harmless ghouls there including Twilight's mother, and then destroy Friendship City just to eliminate one elderly Dashite.
The filly who is terrified of Littlepip, calling her "Hellmare" for what she did in Arbu, runs into the path of an Enclave soldier's disintegration gun and is vapourised. Littlepip carries her ashes around in a bottle as a Tragic Keepsake.
The Everfree Forest is twice as dangerous after two-hundred years to grow into a place where everything wants to either eat, kill, or hurt you. There are Hellhounds, Cockatrices, sentient mushrooms that chase victims and transform into their victims, and the plant equivalent of an anti-air rifle. And then there is Killing Joke, a blue-coloured ivy-like plant that can perform instant transformation on a victim's body or mind, with the end results that double as cruel jokes based on off-hand comments they may have made ages ago. The plant's modus operandi is basically Death by Irony. For example, a Hellhound is transformed into a pony and instantly killed by his fellow Hellhounds.
Fluttershy was transformed into a yellow and pink willow tree by the Killing Joke and placed on a hill able to see Equestria's destruction.
Princess Celestia's final fate. After Luna died, she abandoned Canterlot and destroyed the remaining balefire bombs, but unintentionally irradiated Whitetail Woods and the reservoir of Equestria's main river. She then went to the Single Pegasus Project to control the weather, but due to Rainbow Dash's tamperings with the Crusader Mainframe within, she became trapped in the computer systems unable to do anything but observe her subjects over two-hundred years.
The finale. Littlepip travels to the Single Pegasus Project, ready to put herself into what's essentially an And I Must Scream state, in order to finally move the clouds. It comes across more of a Tear Jerker mixed with Crowning Moment of Awesome, but the buildup is scary - Littlepip never outright says, or even thinks via internal monologue, what she's planning to do. Just hints, so even the readers aren't sure what's going on; the way she thinks it, it can be interpreted as anything from just another mission to a suicide attempt (her occasional remarks to herself that, soon, she can rest for a long time, don't make it any less scary). It isn't until Calamity figures it out that the readers are finally treated to the truth...and then they have to watch Littlepip send herself to a lifetime of just being trapped like Princess Celestia, albeit with more control over the weather. Sure, it's mostly Tear Jerker, but the nightmare fuel is still there.