- How the Alicorn Amulet was created in The Forgotten Darkness. The Tricksters lured the Jackhowls into a trap, and when Sharp Paw told Dark Mist that he connected his aura with every Jackhowl, Dark Mist then reveals that this was exactly what he was hoping for, and uses a connection rune to connect himself to every Trickster, and Sharp Paw, then signals Vile Rune to start the ritual, which kills every Trickster and Jackhowl in existence.
- The flashback in chapter 5 of The Knight of Friendship. It starts out with Cold Steel and his parents tending a greenhouse, but when they exited it, they saw that the village was on fire. The village was attacked by bandits, and everyone, including Colds parents were killed, and they were about to kill Cold too. He barely managed to escape, but only by killing them first.
- Gold Hoof's death in "Building Bridges". Even if he completely deserved it, being blown up by a magical symbol put on him by his mysterious business associates is still a nasty way to go. It doesn't help that he realizes what was about to happen and begs for Flash and Cold to save him before it goes off.
- The initial nightmare Flash suffers from the Tantabus during "Do Princess's Dream of Magic Sheep". He watches all of his friends die right in front of him, lightning sticking all the homes in town and turning his friends to dust before his eyes, and he hears their voices taunting him over how he failed them and couldn't save them. Though things take a major Mood Whiplash when his true worst fear is revealed, it does little to diminish the experience he went through before Luna and Trixie arrive to help.
- "The Day Flash Sentry Died" is easily the darkest chapter in the series.
- The chapter introduced us to the Flos-Mortem flower. It is a plant with a pollen that is so deadly that anyone who takes just a mere whiff of it will die instantly. Worse, just a minor disturbance of the flower will cause it to release its pollen no matter how small it is, like when a ladybug landed on the thing and got a full blast of the pollen, killing it instantly.
- To make matters worse, it almost kills Flash. And if that wasnt enough, not even the Sacred Light can stop it, as all it can do is delay the effects. The fact that the Sacred Light couldnt stop the poison all but implies that the Flos-Mortem flower is a creation of the Corrupted Shadow.
- The effects that the thing has on Flash, as the Sacred Light tries to hold back the poison. Flash suffers a Dying Dream, where he was never adopted by the Sparkle Family, and spent his whole life being treated like dirt from everypony, no matter how much good he tried to do. Eventually, he comes very close to just giving up, but fortunately, thanks to his friends getting the remedy in time, as well as calling out for him is able to prevent him from dying.
- One of the timelines that Twilight and Spike traveled to in "The Cutie Remark", was one where half of Equestria was covered in Flos-Mortem flowers.
- The final part of "The Lost City" officially introduces the showy villain that had appeared several times before and the minions he had spoke of previously. The whole thing consists of them hunting down a single Canterlot guard pony who had discovered their base, with it being not so subtly implied that they had already killed the rest of his squad. Each of them gets a moment of showcasing their abilities and torturing the poor guard, until their master appears to finish the job.My name... is Shadow Corrupter. The most powerful pony in Equestria.
- The Adult Fear of Fire Heart and Shining Soul, two young kids, being stuck in the city of Faust by themselves for three years. They don't even know how they got there to begin with, they just woke up one day and found themselves there all alone.
- Searing Salix being Reduced to Dust during a battle against Flash's team. All of his teammates are shocked by it, with even Shadow staring at the sight in shock. The same fate almost happens to Soarin too, before he finds a strange sphere and touches it, which ends up saving him and winning his team the battle. It is revealed in the next chapter that Salix was actually still alive, but this does little to diminish the actual act, and it still happens to two others before the reveal is made.
- The Cult of Shadow show no problems in harming children, when they attack Shining Soul despite the fact that shes only a filly. It gets even worse when its revealed that shes an alicorn, which causes them to become even more determined to kill her.
- Flash's team get a hint of what happened to the City of Faust with a journal Trixie found and Flash translates. The city was ravished by an unknown plague, and everyone was put under quarantine, explaining the bubble around the city preventing them from leaving. Apparently, only children were immune to the disease for unknown reasons and they were sealed away in bubbles and put to sleep to hopefully live their lives in the future when the plague died out. But this also implies that Fire Heart and Shining Soul were the only survivors since they haven't seen any other foals since they woke up in the city three years ago.
- Shining Soul is chosen to fight for Team Flash once again. Things are made even worse when it is revealed that Shadow Corrupter was one of the fighters chosen for his team, and with Terror Card and Searing Salix keeping Trixie and Ruby busy, Soul is left all by herself against Shadow, with her just trying to run away from him and hide.
- A flashback reveals that Shadow Corruptor is the way that he is now, because he was groomed by the Cult of Shadows as a colt to serve as the vessel for the Corrupted Shadow in a sacrificial ritual.
- In the final clash against Flash and Shadow, Shadow says how he wants Flash to stay alive just so he can watch him conquer Equestria, and he will be sure to make sure everyone knows everything they suffer will be Flash's fault for failing to save them. He also explicitly says he plans to slowly drain Twilight of her magic, and if she survives the process he will find other uses for her, like as a replacement for Tempera. This basically means that Shadow was planning to turn Twilight into a Sex Slave, just to spite Flash.
- In "The Next Generation of Aura", Shade has escaped from prison, just like he promised.
- In "Amber Alert", Flash and his team encounter a creature called a Loucarcolh, a giant snail-like monster with razor sharp teeth. Its lair is filled with the bones of its victims, including the missing livestock from New Omniara and several missing ponies as well. It manages to capture most of Flash's team, and would have most likely given them a similar fate if not for Flash's quick thinking.
- In "The Bug and the Knight", Flurry Heart is almost kidnapped by a mysterious assailant in the middle of the night, with her only being rescued because Thorax and Hiveena just happened to be walking by together and hear the commotion, leaping into action to save her. Then not long after this incident, the one who hired that assailant, Hard Sell, attempts to murder Flurry Heart himself, due to believing that she is too dangerous to be kept alive with her powers at her age and could destroy Equestria if she goes down the wrong path. Though the combined efforts of Hiveena and Ruby prevent this, the event reveals to Shining Armor and Cadance that other ponies are also afraid of what their daughter could become, showing what Flurry will face as she grows up.
- In "The Trial of Flash Sentry", Mecha-Flash is this as he was unstoppable and no ones could keep up with him. Doesn't help he had an ability to suck all of Sacred Light from Flash, since it was previously established by Faust that removing the Sacred Light from him could potentially kill him.
- In "To Where and Back Again Part 1", Queen Chrysalis is even more dangerous than her canon self by not only kidnapped Mane Seven, Defenders, and the Royal Family but the entire Royal Knights!
Nightmare Fuel / The Flash Sentry Chronicles