This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Warframe
Despite the Tenno who would win any fight despite outnumbered 100 to 1, gain their insane powers from the Void that is described to be the place where logic fails, there are things like Stalker, the Grustrag Three or the Lephantis. There are even more bigger fishes than these super-soldiers.
Even so, some Tenno are more than a match by themselves for the enemies mentioned above.
In a similar vein, the way Capture targets howl in pain as you capture them. Were it not for the Stolen Dreams quest, you could be forgiven for thinking you were subjecting them to a Fate Worse Than Death simply with the "teleportation", especially since the Grineer have already proven faster/less painful teleportation technology exists.
The Stalker, if you aren't expecting him. You're out, minding your own business, celebrating a boss' defeat, when suddenly, the lights flicker. Then:
Stalker: [Player], you cannot run from your past.
The OrokinVoid. Pristine. Beautiful. Transcendant. Utterly empty except for "corrupted," nearly-silent versions of enemies you face in normal levels. No music plays during these levels. Look out a window and all you'll see is black dots in an endless white expanse. It begs two questions - who were the Orokin, and where did they go?
The Orokin Void tileset now got their own soundtracks, and the creepiness might just be worse since it's mostly Ominous Latin Chanting.
The Zanuka Project: various sliced-up Tenno and their warframes formed into a mechanical quadruped controlled by Corpus technology.
Valkyr, the Warframe produced as a byproduct of the Zanuka Project. All subsequent Valkyr frames are based off of the template of the original. It's impossible to tell what frame Valkyr used to be, or if we've even seen it yet, but that's not even the scariest part. Given that Warframes draw their power from the Void in a manner that is suggested to be intrinsic to their psychology and outlook on life, it suggests that whatever Alad V did to Valkyr caused her psychology to change so drastically it altered her Void imprint.
The Infested. Grineer and Corpus alike who were unlucky enough to get infected, twisted and hideously mutated. Some wind up running on limbs that used to bend the other way; others as eyeless things with no purpose but to get close to an enemy, at which point they spasm and then explode in a spray of gore and nano spores. Some are reduced to just a (mostly) headless torso, pulling itself along with its flailing arms. Pray that nothing of the original mind remains.
The Infested Corpus◊ have a new arm growing from their chest and fused to their face and helmets like it was grasping at their skulls. The Infested Grineer◊, once humanoid, have been twisted into quadrupeds in the grossest way possible, their chests pointing up in the air with their limbs bent backwards and joints inverted, a new "head" forming over their heart while their old skull hangs below their body. As for the Ancients◊, whatever they were before, they have no resemblance to it at all now.
Lephantis, a bio-engineered Infested monstrosity that was created for the Old War and survived by hiding in a derelict Orokin ship. It consumed and absorbed everything and everyone that discovered it, and so when you reach its chamber, it attacks you with giant, twisted versions of all the enemy factions. The Corpus head is especially horrifying, as the infested Crewman's helmet has fused with his skull and become a mouth that opens to attack you (compare a normal Crewman◊ to the mutated version◊), and the Grineer head has a huge scythe which is basically an instant kill. When you defeat the heads, the floor beneath you breaks, and you fall down to see Lephantis's main body, a building sized monster with all three of the heads growing out of it. Only then does the boss subtitle appear. Doesn't help that all the while, Lephantis is sending you messages like "We are countless. Consume us. Be reborn." and "We embrace you. Why do you defile us?".
It gets worse when you're familiar with the lore and realize that Warframes are likely based on the same technology as Infested, supported by the assertions of the Jordas Cephalon in an Infested mission "Tenno, it senses you are of like flesh, it is confused. Why do you defile us?" and "I see it now, you are the same. They fear themselves."
Further supported by the Excalibur Proto-Armor which has the description "Discovering the precise nature of this recently uncovered armored prototype has proved elusive. Initial attempts at dating point to ancient origins, perhaps even predating Orokin Empire." and is a direct reference to DE's previous game Dark Sector, which had a very familiar threat called the "Technocyte Virus" that would take over hosts and warp their bodies, almost exactly as Infested do. In the Dark Sector universe it is nicknamed "The Great Plague" and an infested weapon in Warframe, called the Mire also references a "Great Plague" hinting that these are one and the same, and Warframe technology was based off of the technocyte virus.
At the first day of Warframe, planet Eris was described as the location of far-flung Corpus outpost. Now, every single mission nodes there are controlled by Infested.
On some maps, in missions on planets where there is no Infested invasion, you can find in some innocuous corner somewhere a small patch of technocyte Meat Moss hidden and growing. No planet is truly clean; the Infested have footholds everywhere and will always, always return. The Origin System will never be free of them.
The fact that the video appeared exactly at the end of a developer livestream interrupting it mid sentence without warning increased the effect.
Before the Grustrag Three show up, the Lotus contacts you about 'impossible readings' she is picking up nearby, and her transmission is abruptly cut off. She gets out a few more garbled transmissions about how you are 'being hunted' and then suddenly begs the Tenno to abort the mission now before she is cut off totally. There's a few seconds of nothing, then the Three spawn into the level.
The genuine concern you can hear in her voice is what really frightened me the first time the Grustrag Three appeared in my game. Lotus, while she does care, is nothing but utterly calm, or at most, mildly surprised, even on the most dangerous missions. Suddenly, she is clearly frightened and confused, screaming at the player to abort and run before getting cut off.
Seeing your Warframe getting captured under the orange cage-things is pretty disturbing too, double if you don't know what's happening.
Infested Corpus Ships. They have this music, are claustrophic, full of deadly hazards that get worse as you kill more hive nodes, near-insta-kill poison enemies can trap you at close range, and there are so many infested in your face that you will start drowning in them if you don't have a decent piercing or crowd-control ability. All that's missing is the M 41 A Pulse Rifle.
What's even worse are the Parasitic Eximi that constantly drain your energy and Mutalist Ospreys spew toxin fumes that directly damage your health. If you aren't prepared, hive missions can suddenly become Survival Horror.
Vor's ominous threats and taunts as his Ascaris slowly takes more and more of you over in Update 14, culminating in this line that replaces the Lotus' standard "Mission complete" dialogue at the end of the Corpus Hijack mission.
You are MINE.
Story-wise, the little information we have of the Sentients leans them towards this. These are something so threatening that the Orokin unleashed the Technocyte Plague and the Tenno in order to try and stop it. They pilot "worm-ships" which use heat-bursts to boil their enemies from the inside, are described as having "multi-faceted eyes", and are nearly endless in number.
It Gets Worse; The Tenno were chosen to be used in the war because their powers were spawned from the void— a "hellspace where science and reason failed"— and thus couldn't be subverted by the Sentients, who were getting stronger with every advance the Orokin fielded. Lotus reinforces this in Vor's Prize, pointing out that the presence of the melee weapon was an adaptation to the sentient's ability to subvert technology.
Ember Prime's codex entry implies that the Orokin were so desperate that they even threw kids into the Void.
The Tenno themselves. Almost completely silent killers, who can strike almost anywhere and at any time. Their nature is largely unrevealed as well. All we know is that those who made it back from the void came back wrong. High ranking Tenno can and will single-handedly wipe out entire armies, from lowly grunts to the elite of the elite. The only enemy who regularly gives a well equipped Tenno pause is the Stalker.
What happened to the original Limbo. Specifically, the way it's described to us.
Although, Skates are real animals related to mantas and sharks, and their undersides are quite normal looking◊... compared to other mantas and skates
The cryptic message you find in the Orokin Derelict at the end of the Stolen Dreams questline.
All-All is silent- Hushed-hushed and empty is-is-is the womb of the sky.
All is silent and calm. Hushed and empty is the womb of the sky.
Even creepier? That's from the Popol Vuh, a real-life Mayan text that details their creation myth. Those lines were used to describe the 'primordial world', what existed before the world itself was created.
You have read all of the entries here yes? The Sentients are returning.
Unless you've seen the trailer for Tombs of the Sentient, you won't know when Teshin, the Conclave master, references them. All you'll know is he's trying to prepare you for the evils returning from beyond the outer terminus.
Need we remind you again that the relic you interact with in Second Dream quest is corpse of Lotus' father? Yes, that one gigantic pillar stuck underwater allllll the way up to the surface is only a part of it!
How bad it got? They converted the Stalker to their side!
Grineer Manics. You're just going about a mission, happily killing things until you start hearing this insane laughter and then these things show up. They can be seen as mini-Stalkers, seeing as they can turn invisible and invulnerable,can regen health, can Dispel your abilities, and can easily kill you if you're not cautious.
The Blackout tactical alert. There are no enemies until you reprogram the navigation computer. Then 75 Grineer Manics appear out of nowhere...
Then there's the fact that the warframe that was just described as a mindless machine, takes War, the current source of the Stalker's power, and breaks it.
The premise. You spend quality time with your nice and cozy warframe then you got decked back out into your unfamiliar body, dazed and confused, while a dozen Sentient are out for your blood...
The Orokin. Just the Orokin. Each new bit of lore focusing on them reveals a new, incredibly disturbing level of dehumanization, scientists with Morally Ambiguous Doctorates, and incredibly unethical experimentation.
Which gets even worse when it's revealed that the Tenno are Child Soldiers who haven't aged a day since they entered cryostasis centuries ago. The Orokin considered it acceptable to take casualties from a horrific Teleporter Accident and turn them into soldiers just to make use of the destructive powers the Void gave them. These silent masters of warfare, capable of slaughtering absolutely anything in their path, are less than seventeen years old when they finally wake from stasis. And they've experienced all those battles as if they were these in person, thanks to their Warframe proxy units.
Lately (as of March 2016), players will find Infested tumor inside their orbiter.