The acid fog in "Earth Kills": A storm of toxic fog that viciously burns anyone exposed to it. It leaves Atom in such unimaginable pain that he begs to be killed.
Charlotte's murder of Wells is particularly unnerving. She sits down next to him on watch, and he is nothing but friendly to her. She then cuts his throat when he turns away (copying Clarke's Mercy Kill of Atom) and then wildly slices at him as he tries to fend her off, which ends up cutting off a few of his fingers as he dies. Then his body has vanished by the beginning of the next episode, leaving only his severed fingers behind for Clarke to find.
The torture of the Grounder Lincoln is particularly harrowing- he is beaten, impaled and electrocuted over the course over a very long night. Moreover, his refusal to break could have led to him being tortured to death.
Bellamy's vision of Jaha and every single member of the Ark who was killed because he destroyed Raven's radio haunting him and calling him a murderer. The blood spilling out of Jaha's chest makes it all that much more terrifying.
You know the Grounders, those tough, ruthless warriors who view charging the 100 in their fortified position as a challenge worth taking? Who view the fact the 100 have automatic weapons as a minor hurdle to Victory. Stealthy, quick, strong and relentless? Meet the Reapers, who view Grounders as walking meals. And who when even if their is a hint of them in the area , will cause the Grounders to run for their lives dignity be damned. The fact that they are animalistic, brutal and like their meat fresh may have something to do with it.
The season one finale enforced this when a Reaper hunting party comes across an Grounder invasion fighting force, and despite being outnumbered at least three to one held their own for at least five minutes.
At the end of "We Are Grounders, Part Two", we finally get a look at the "mountain men" that The Grounders dread so much. Men in sealed suits, wearing gas-masks, with knockout gas grenades and rifles with laser-sights. They capture The 100 and hold them prisoner inside Mount Weather. The fact that they appear to have treated the 100's wounds mitigates this slightly, but they're still scary as hell.
Clarke herself in the first episode of season 2. She holds one person hostage by the throat, cutting into it, and then tries to escape by opening a hatch, knowing that the radiation will kill them. Note that she doesn't have much reason to doubt their words, but her time outside had left her so paranoid that she kept trying to run.
Raven needs surgery or runs the risk of never walking again. Unfortunately they don't have any equipment or way to numb the pain means its a Meatgrinder Surgery. Her screams echo around the camp the entire time.And even with the surgery she's still crippled enough to need crutches.
The Grounders crucify a number of people just outside the camp of the Ark survivors to send a message.
The secret behind Mount Weather's medical treatment? They capture Grounders, harvest their blood, and then drop the corpses into the tunnels where the Reapers can get them. Worse, some of them are still alive when the Reapers get to them.
In "Spacewalker", Lincoln's description of a Grounder execution is...unpleasant, to say the least. First you get burned, then parts of your body are systematically removed one by one. At sunrise, the commander comes and finishes it with her sword, but nobody's ever made it that long before.
Clarke spends the entire episode after she kills Finn hallucinating him, but the worst time is the first. She's looking at his dead body when his eyes snap open and he stares at her as he is carried away by the Grounders.
The gorilla that mauls Grounders and chases Clarke and Lexa.
Anything to do with the marrow transplants conducted by Doctor Tsing can be pretty terrifying. Seeing some of the scars on one of the survivors and seeing the blood-soaked wrappings covering bodies of the deceased is absolutely revolting, especially considering the implication that the victim is alive and conscious throughout the process. In addition to their Grounder farming and the Reaper training, it's made pretty clear that Mount Weather is perpetrating some serious Medical Horror to achieve their goals.
It was worse in Second Season Finale. We see them going through the remaining kids one-by-one without remorse, leaving corpses behind despite them screaming for the pain to stop.
Especially because this is usually accompanied by a close-up shot of the drill boring into the flesh. Being stabbed would be bad enough. Having the knife twisted would be worse. But having a piece of metal whirring through your flesh into your bone, so they can kill you piece by piece?
Dr Tsing dying of radiation poisoning in the corner of an elevator, cornered by Jasper and his friends. Yes, it was incredibly cathartic, not to mention deserved, but still...
The climax of the Season sees Bellamy and Clarke jointly commit genocide by irradiating Mount Weather, killing not only their enemies, but all of their allies within the mountain who were honestly trying to help them, including Maya.
The last moments of Season 2 Murphy finds a video recording of a man claiming it was his fault that she got the launch codes before shooting himself in the head. Then Jaha finds a women in a red dress in the mansion who is a projection created by a AI which thanks him for his gift. Jaha enters the next room and finds the missile he used to get to earth with the AI calmly stating they have work to do
Murphy going crazy from the isolation of being sealed in the bunker for over 80 days is nothing short of disturbing.
We actually do see the City of Light... It's a drug-induced hallucination, leaving Jaha and two Grounders he "recruited" in an eerily relaxed state. The AI from the end of season two, Alie, even speaks to Jaha through the hallucination, asking him to bring "his people" to the city. Murphy was right for not buying into it.
How quick Otan was ready to kill Emori, his own sister, after a single trip to the City of Light speaks volumes about how powerful A.L.I.E's control over her recruits is.
Gina gets brutally murdered by an Ice Nation warrior, stabbed multiple times in the stomach. It only gets worse from there: The warrior activates Mount Weather's self-destruct sequence, killing all the Farm Nation survivors inside. Gina doesn't even die right away - she dies slowly, weeping, trying in vain to hang on long enough for Raven to call back with the deactivation code.
Emerson survived after the irradiation of Mount Weather... And is now working with the Ice Nation.
Charles Pike is about to start a war against the combined might of the Twelve Clans. He's basically signed Arkadia's death warrant, since even with guns and ammo, the Clans can still overwhelm Arkadia with their much larger numbers.
Otori revealing that she has "won" the conclave by murdering the other Nightbloods - all children - in their sleep, by dumping their heads out on the throne room floor.
Jaha reveals just how the City of Light tablets remove people's pain: they rewrite people's brains so any physical or mental pain simply has no way to get in. And just how bad this can be is shown immediately afterwards when Abby asks if he would let his long dead son take them, and Jaha responds like he's never heard the name before.
The flashbacks revealing how the world ended as it did: Becca informed by aide Chris that Alie has gotten loose and hacking defense systems. Remembering Alie's words of "too many people," Becca tells Chris to send out the killer virus to wipe out Alie only for Chris to choke out that "I did that 10 minutes ago" and it's not working. He goes to shelter as Becca is informed of massive nuclear launches and looks down from the space station to watch as her creation destroys humanity.
ALIE shows just how thin her conception of free will actually is when she utterly breaks Raven by repeatedly torturing her with the memories of losing Finn, her surgery with no anesthetic, and being drilled into for her bone marrow at Mount Weather.
And how this changes Raven. She's just... gone. And instead, ALIE is puppeting her body. Lindsey Morgan (Raven) perfectly imitating ALIE's body language, with Erica Cerra's (ALIE's) voice coming from her body, is complete uncanny valley nightmare fuel. This while ALIE makes Raven slit her own wrists to force Abby to take the City of Light pill. Her behavior when tied up at Nylah's house is especially creepy, in a distinctly exorcist sort of way.
Kane returning to Polis with Pike, after ALIE has taken over, and finding the streets literally red with blood from the people who are crucified for refusing to join ALIE.
In the season 3 finale, we finally learn why ALIE has done what she's done. She's not attempting to control humanity or start another war, she's giving humanity a Mercy Kill. The nuclear power plants that she hit in the first nuclear war have begun to melt down, and within six months the Earth will become uninhabitable due to the radiation. At least seven are already burning. And with ALIE gone, there might be no way to stop it.
While it's good to see the people finally freed from ALIE's control, it also means they feel the massive pain they had ignored of lost loves and such. Not to mention now the guilt over their actions under ALIE, from torturing to even killing friends.
The first scene of the fourth season shows the immediate aftermath of everyone freed from ALIE's control. Jasper in particular is close to suicide after all he's done.
Ilian's introductory scene, in which we watch him, chipped, murder his brother and father and torture his mother to try to get her to take the chip, only for ALIE to vanish when Clarke pulls the kill switch...leaving him to suddenly see what he has done, just in time for his mother to die of her wounds.
Season 4 introduces the black rain, which burns on contact. Lengthy exposure results in radiation poisoning and death. Roan's death via black rain is particularly horrific, as he had previously been beating Luna, but since she is a Nightblood and is immune to the rain, he is ultimately taken down by nature. She finishes him off by drowning him in the poison rain which is simultaneously burning his skin and poisoning his lungs. Not a fun way to go.
Then Season 5 brings us parasitic sand worms that borrow into people, make their way into their stomachs, and then eat their way out.
Clarke mortally wounds one of the Eligius Prisoners by baiting him into a trap that holds him in place with a dose of Impaled with Extreme Prejudice, only he's still alive afterwards. Then she starts trying to snipe the other prisoners who try to come to his aid as he screams in pain.
Octavia reinstates the rule from the Ark that All Crimes Are Equal, but instead of floating convicts, she gives them a chance to survive in Gladiator-style fights.
In what Wonkru called the "Dark Year," those who were waiting out Praimfiya in the bunker had to resort to cannibalism in order to survive after a food shortage.
Not only that, but one Grounder was forced by Octavia to eat his own brother at gunpoint.
It is revealed that the "Naming Day" for someone with Nightblood (termed "royal blood" on Sanctum) involves using chips ("Mind Drives") which completely overwrite any person's existing personality and memories (very similar to ALIE 1.0's ability to delete/suppress memories, and render a person nothing but a vessel for her to speak from), all so people who lived 200 years before can ensure their immortality for as long as black blooded people continue to be born.
Clarke's 'death'. She is paralyzed and unable to do anything but watch as Russell thanks her for her (completely unwilling) sacrifice and plunges a needle into her neck.
The Hall of the Primes. In the interior of their castle is a circular chamber, with a series of skeletons standing in lines from the center outward. Each of the skeletons has a plaque by their feet with a name, such as "Russel IV" or "Simone II". Everyone is pretty weirded out by it, but the horror doesn't set in until Bellamy realizes it's basically a massive display of all the the Primes' former "hosts", i.e. people who they basically murdered and stole their bodies to use.
Clarke brutally kills Josephine at one point by slamming a door on her head until it bursts. Even though Josephine is immediately resurrected by the mind drive, it's quite unsettling to see.