Blackjack gets a first-hand view of how the Enclave markdashites. Their cutie marks are burnt away by chemicals strong enough to produce smoke, and the fresh wounds are then immediately branded. Worse, this happens to Morning Glory, arguably the most moral character in the story, who is completely loyal but being set up for political reasons.
Enervation. It's completely undetectable, except through its effects, and even minor exposure is enough to degrade healing supplies over time. More serious exposure results in internalbleeding, and existing wounds worsen rapidly. At high concentrations, victims suffer from Mind Rape and melt.
Enervation is practically alicorn kryptonite. They percieve it as a constant psychic screaming which breaks down their Hive Mind. Only Lacunae is resistant (but not immune) to its effects,note Emphasis on "only"; the reason it causes so much damage is because if there's two or more Alicorns present, the screaming will echo between them until they shut down. and even the Goddessis tormented by it. When Lacunae is briefly exposed to an Enervation source at close range, all of Unity is injured by it.
Stable 90 was registered as complete and ready for habitation, despite having none of the essential fixtures or equipment installed. When the bombs fell, the residents were trapped inside, descending into barbarism and dying off completely in under a month. The ponies of Stable 99 would have suffered the same fate if Blackjack hadn't gassed them all.
Rampage: You want fear? Fear is being strapped to a table as a permanent lunch for a bunch of cannibals. Knowing they’re going to rip you apart and eat you over… and over… and over again. Fear is knowing you might spend years or centuries that way, your flesh fueling the nightmare and you helpless to stop it.
All of final scene of Chapter 26, especially Glory's wing falling off, and her reaction to it.
Chapter 30, where the taint building up in Blackjack's body causes a tumor to grow in her eye socket, forcing Glory to perform emergency surgery and get it out.
Horizon Labs' cryo room, where a number of ponies have been melted and fused with the walls and equipment, screaming. The room is practically soaked with taint, and tries to absorb Blackjack, almost succeeding. Now illustrated.
Chapter 33 begins with a disclaimer warning readers of a particularly brutal scene. Said scene involves Blackjack, who is blind and practically immobile, being mutilatednote - her useless, mutated legs are nailed to the floor and her horn is smashed off - and gang-raped. The entire ordeal is narrated from BJ's sightless first-person perspective. There is no Rape Discretion Shot (though the hour-long ordeal is summarised in a couple of paragraphs). Scotch Tape, who is hiding in the hold below, overhears everything.
Priest's death at Sanguine's hooves. It brings to mind this◊ (NSFW and graphic) picture of a Hiroshima survivor.
Blackjack's encounter with pink cloud results in a fair degree of Facial Horror, including a self-inflicted Glasgow Grin after her mouth is fused shut. Illustrated here◊. (NSFW, bloody)
The visual representation of Blackjack's traumatised, suicidal mind.
'Glory': It doesn't have to be dark. Your subconscious is... terrifying.
Hightower. A fortified prison filled with thousands of ghouls, most of them trapped in their cells. Not all of them are feral. The building's also bathed in powerful enervation fields and radiation, not to mention the sentient acidic ooze living in the plumbing and the malfunctioning balefire bomb in the central chamber. It's also on fire.
In Chapter 62, Blackjack voluntarily - though not willingly - enters Lighthooves' cyberpony enhancer and "upgrades" herself to a cybernetic alicorn. This despite her knowledge that Cybernetics Eat Your Soul. She's fully conscious while the device implants wings into her back, strips the skin off her face and covers almost every inch of her with metal plating.Yikes.
Also from 62, the implosion megaspell that Blackjack sets off. It creates a massive vortex that is enough to destroy practically all of Shadowbolt Tower - a monstronsity whose size can be measured in miles - and crushes it into a little sphere.
The fates of the members of Macintosh's Marauders are at first considered coincidental, but it turns out they were the downside of a Deal with the Devil the platoon made with a zebra fortune teller to avoid a pitiful fate. The zebra used the Black Book (yes, that Black Book) to alter their fate but warned them if they broke their fellowship, they would each suffer a Fate Worse Than Death while the culprit would die peacefully. Big Macintosh ultimately seals their doom by planning to retire and start a family, leading to nightmarish fates for his comrades when he performs Heroic Sacrifice during the Battle of Shattered Ridge. Blackjack discovers what happened to each character during her journey - Stonewing, Jetstream, Vanity, Doof, Twist, Applesnack, Psalm, and Echo.