The Gorgon Medusa, by far the most horrifying and tragic of the four Mythical Creature Bosses. To wit, she was a Daughter of Artemis named Ligeia in love with a civilian from the nearby town, Bryce. After helping slay the original Medusa and save a mercenary, ended up being turned into her replacement after touching the Piece of Eden. Bryce's desperation to find her again, and her pleas for her to please just come back to her during the run through the Petrified Temple are heartwrenching, and the transformed Ligeia petrifying and shattering her all the more terrifying. Worst of all, though? Bryce still recognized Ligeia in her Medusa form.
The way she moves is deeply unsettling too. Every attack she throws is jerky, almost giving the impression of a corpse being puppeted with strings. Given the fact that she was Ligeia, that might not be too far from the truth.
The Swordfish, local crime boss of Heraklion, and a former member of the ill-fated Minotaur expedition. He has the entire village cowering under his reign of terror, enforcing it with armed thugs. He has a hair-trigger temper, having cut off one person's nose simply because they sneezed in his presence. He's also gone completely insane from his run-in with said Minotaur and now hides in an underwater cavern, obsessively chopping up people and throwing their body parts into the water for shark chum.
It's pretty unnerving seeing how frightened of the Minotaur the Swordfish is. Here is a man who inflicted all manner of evils upon innocent people, yet he's terrified at the prospect of this monster escaping from its labyrinth out into the world. It becomes a case of Horrifying the Horror and many first-time players will no doubt be left frightened by the idea of the Minotaur if it can scare so foul a person.
The Labyrinth itself is also genuinely creepy: dark corridors, mutilated corpses—some of which look like they may as well be inside-out—the ominous bellows of the Minotaur itself from the center, and you can't even climb the walls to try and get your bearings like you would almost anywhere else in the game.
Deimos, both conceptually and in-universe. This was a baby stolen away by a fanatic cult eager to rid the world of Leonidas's bloodline, and brought up as a weapon solely for destruction. If not just for the fact that the Cult of Kosmos stole Deimos away from the Eagle Bearer and their family, they first had to create a false prophecy in order to take them away, then convince Myrrine that the baby had died in Argos, then force them to undergo training from Hell in order to not only make them a living weapon, but a brainwashed servant of their own bidding that even the Cult couldn't control. There's a reason that Deimos means "terror" in Greek, after all.
With patch 1.20, a new quest has a moment where you get to momentarily play as Deimos... as they brutally beat down an associate of the Eagle Bearer for information, start by smashing his head against the near surface, followed by stabbing him, followed by just beating him to death. Just to twist the knife a little further, you (and by extension, Layla) can try to refuse to do it... the conversation just resets and makes you continue. For Layla it makes him more frightening because by way of the Animus, she's forced to enter and re-enact the psyche of a complete sadistic lunatic, which can be a huge whiplash if she's been playing a benevolent and kind Eagle Bearer.
Chrysis. Holy shit, Chrysis. She's the reason Deimos turns out so cuddly, and just five minutes in her presence is enough to see how that could've happened. Probably one of, if not the most despicable beings in all Assassins' Creed, she's a psychotic maniac just barely hiding behind the image of a respected priestess. Try to confront her, and she kidnaps a baby from her mother and holds it hostage, making the Eagle Bearer chose between killing her or letting the baby burn (mom's view on all this if you save the baby? "Well, she knew what's best.") She even wanted to abduct the Eagle Bearer's mother and turn her into a baby factory for the cult.
If you're afraid of snakes, then Agamemnon's Tomb will be truly terrifying for you as once you've found the ancient stele, the only way out of the tomb is through a dark pit that contains at least 20 snakes. There's a platform you can stand on and fire at them with arrows where they won't be able to reach you, but the hissing you'll be hearing during this will send shivers down your spine.
On the topic of snakes, there's also the Snake Temple in the Valley of the Snake in Phokis. A first-time player might not think anything of the names, but upon arriving will be greeted by an absolutely massive snake skeleton coiled around the remains of the temple. It goes completely unexplained and the Eagle Bearer is so unfazed by it that they don't even really acknowledge it.
In "Heir of Memory", there's some updates to the modern segments, including emails from Otso Berg to Layla. One of them is a hint that Dana is alive, and in Abstergo's "care". How? Berg refers to Layla as "habite".
Also, in "Heir of Memory" there are hints, just hints, that Alethia isn't as benevolent as she's appearing to be.
There’s a cave in the Torment of Hades simulation called Cradle of the Underworld. It’s meant to contain the souls of infants who died before they were born. For the most part, it’s is like any other one in the DLC, except for a room filled with tombstones. Listen closely and you’ll hear the wails of a crying baby that will certainly send shivers up your spine. The sound can’t be heard in any other part of the cave.
By the end of the second episode of Fate of Atlantis, Layla has absorbed a lot of knowledge about how to wield the Staff of Hermes Trismegistus, the powerful Isu artifact. Unfortunately, a little (or too little) knowledge is a dangerous thing, as Layla's colleague Dr. Victoria Bibeau realized and Layla horrifically found out; corrupted by the otherwise-benevolent Staff's influence, Layla refuses to give it up and, with it, gives Bibeau a smack upside the head and sends her across the chamber, breaking her neck.
Remember that bit up above about the Medusa? Well, Fate of Atlantis brings you the origins of the Olympus Project that spawned her, and the lovely minds behind it. Or as Assassin's Creed fans know them, Aita and Juno. And it turns out they're even sicker fucks that might've previously been guessed, having abducted and experimented on dozens (if not much more) of humans to create these things. And why? To scare humans into permanent obedience.
The lab itself is already disturbing, as the Eagle Bearer walks past a jar, then does a double-take at seeing the Minotaur floating there. Then they look around and see the Cyclops, Medusa and the Sphinx just floating there. In the room beyond are yet more of Aita's "experiments": Zombies. Which will randomly explode. And there are a lot of zombies...
The final boss of the DLC, the pinnacle of Project Olympus, is Juno and Aita's secret weapon. Before the Eagle Bearer interfered, they planned to release this monster and instill profound fear into the Atlanteans and human residents alike, securing eternal worship for them. A massive, multi-limbed creature (five wiry arms sprouting from its back, along with two heavily muscled ones), cobbled together from multiple human subjects, it is the Hekatoncheir. The only-vaguely-human beast acts more like an organic automaton, repeating horrific lines pronouncing death and destruction upon the Eagle Bearer, and if the other Project Olympus "successes" are any indication, perhaps it's a blessing that all we see of its face is a curved slab of Isu metal welded onto the front of its head. Oh, it also summons lots of those exploding zombies during the fight, too.
Inside Aita's lab, he offers the Eagle Bearer a choice: Let the humans he's experimenting on go free, or... see what's behind the door he's standing in front of. Of course, do that and all the humans locked up will die. And it's Aita, so you know whatever's behind that door is going to be monstrous... do it, and you see what's there: A dozen clones of the Eagle Bearer. Aita and Juno have been breeding clones of the Eagle Bearer, with the plan of putting their minds into their bodies, to wipe out mankind. Making it worse, the clones don't attack you, they just stand there... staring at you.
Opting to side with Anthousa and killing the Monger in public, but the Eagle Bearer refusing to kill him him/herself. Anthousa and the rest of Korinth's hetairai will all draw daggers and begin stabbing him to death at the same time. The Eagle Bearer will then turn around to walk away only for a severed arm to be flung through the air and land right in their path.
On the flip side, earlier in the Questline, you can find The Monger's sex dungeon at the behest of one of the Heterea who was set to be the next unwilling inhabitant. That alone is disturbing enough, but inside you find chains and blood—suggesting his last victim didn't survive their time there.
Mounted on the back wall, the Eagle Bearer can also find what appears to be the casts of a couple of women's faces and breasts. While its possible that it's just erotic art, the Eagle Bearer's horrified reaction to it suggests that its likely more sinister than that—potentially being casts of the Monger's former sex slaves that have since been murdered.
One of the Monger's mooks will find the Eagle Bearer after their investigation, tossing Phiobe at their feet. It's unclear if he brought her there because he knew there was someone inside, or because he planned to lock her there. He does, however, suggest that that is exactly what is planned for Kassandra/Alexios. Thankfully, he's easily dispatched of and the player never has to find out.
The whole implication of this quest is terrifying. The mook implies that anyone at all who catches The Monger's eye is brought there. Each and every person walking around in Korinth could be a target, dragged off to a torture dungeon to be sexually abused for as long as the Monger felt like it, murdered and made into a souvenir on the wall. Worst yet, the open door is right there, taunting the victim with freedom. As brutal as Anthousa's method of execution is, The Monger wholeheartedly deserves it.
