This is based on opinion. Please don't list it on a work's trope example list.
Nightmare Fuel / Defiance
Datak's rage after killing the Spirit Riders is really disturbing. His spitting and inhuman hissing is very unsettling.
We get to see an Earth Republic prison camp in Season 2 - inmates are kept in a large pen, open to the elements, and "fed" by being tossed scraps of food that they're left to fight over.
Irisa's Imagine Spot toward end of "The Opposite of Hallelujah" is definitely this, as they ride together in the dark, father and daughter finally reunited, and then she casually reaches over and slits Nolan's throat. This, plus her murder of a random Castithan woman back in AngelArc, indicate that the Kaziri has done something very bad to her mind.
After being forced by Irzu to murder poor, innocent Bertie, Irisa tries to break free of Irzu's control by shooting herself in the head with a rifle. She manages to pull the trigger, but it doesn't kill her. It does, however, blow a nasty hole in her usually lovely face. Good Thing You Can Heal...
And then the situation gets even worse with the reveal that Irisa hasn't been killing people as she thought, but is instead carrying out some sort of Assimilation Plot involving metal tendrils moving from body to body via the mouth. Pleasant dreams after that.
Datak gets out on probation. Having learned that Stahma has been taking over his business in his absence, he promptly returns home and makes a brutal attempt to drown her in the family tub.
He actually gets creepier in the following episode, trying to reassert his authority by doubling down on Castithan traditions. Fortunately, this is quickly derailed when Stahma has him beaten to a pulp for scarring Alak and takes over the business.
"This Woman's Work" features the first appearance on the TV show of a Gulanee, and it (she?) is terrifying. Clad in an Uncanny Valley-inducing robotic containment suit, with a shriek like a banshee and a touch that fries flesh. Further, our heroes didn't even try to reason with her. Either the Gulanee are too alien to communicate with, or they just don't care.
"If You Could See Her Through My Eyes" features honest-to-god cornea harvesting. They even show it from Rynn's perspective. Try not to cringe. Try and fail.
There's something very...unsettling at watching Christie imitate Stahma's mannerisms, even taking her name. She does it a little too well.
On top of that, she's chumming around with a man that's twice her age, if not more. There is so much squick in this... Creepier still is the fact that he seems to realize as much, but then just goes with it.
In "Painted From Memory," while talking to Pottinger about lobotomizing the Kenya clone, Yewll gets very scary for a moment. We catch a brief glimpse of the Retired Monster behind her eyes, and we remember how dangerous she really can be. So much so that Pottinger actually takes a step back from her out of fear and revulsion.
Pottinger: Doesn't it bother you? Yewll:(Death Glare) I've done worse.
In "Doll Parts", not only does Christie turn out to be the one who killed Diedre and framed Alak for it, but when she admits it to him, she's completely calm, even copying Stahma's mannerisms while doing so. She then basically considers herself a Castithan woman, and gains Stahma's theme song. While also an awesome moment, it's all very disturbing.
"The World We Seize":
It finally introduces us to the Votanis Collective, in the form of Rahm Tak. He's a brutal, imperialistic monster who likes to collect Human body parts. And he promises just to be the beginning: with the Earth Republic all-but done, the VC is start to make inroads into North America...and they have no interest in playing nice.
The Omec. "Dread Harvest" is what the other Votans used to say when they would show up at the other planets, since captured Votans were either enslaved or eaten - usually when the Omecs got bored. It's just as applicable in this case, too; once they manage to power up their ship, they'll awaken what appears to be thousands more in stasis.
Don't forget the fact that they're insanely strong, and have been implied to have created the Indogene species. Which lead to a rather graphic scene of Yewll getting a decent chunk of skin taken off in order to heal an Omec.
Amanda finding out just how far the depths of Pottinger's obsession with her could go, in "Dead Air".
Singularity bombs. Portland, Oregon? Nolan says, "Yeah, I saw the crater."
"History Rhymes": Alak escapes Rahm Tak and makes it home... and then he draws a knife on Stahma, angrily dismissing her protests and excuses. He's fully prepared to kill his own mother to avenge his wife. The kind-hearted young Castithan who married for love and didn't want to follow in his father's footsteps is dead; Alak is now truly Datak's son.
Stahma's situation keeps going from bad to worse: a fugitive in Defiance, she has no choice but to seek refuge with T'evgin. He treats her kindly enough, but more like a pet and/or sex toy...and he keeps leaving her alone with his Crazy Jealous daughter, who's taken every opportunity to terrorize Stahma.
T'evgin killed a VC officer the old fashioned way: By opening his jaws like a snake, revealing his fangs, and chomping down on the officer's neck, killing him graphically and leaving a bloody Irathient mess on the floor, showing who really is the dominant predator of the former Votanis system.
"Ostinato In White":
Kindzi's murder scenes and the aftermaths. Those dismembered bodies are undoubtedly among the most brutal things ever shown on the show.
Yewll under the influence of Kindzi's Indogene control device. First she's nearly forced to cut off her own hand with a pickaxe before Tev'gin stops her, then she violently attacks Samir with a syringe, potentially killing him, in order to obey Kindzi's last order.
"When Twilight Dims the Sky Above":
Nolan's Sanity Slippage continues from Tear Jerker territory into this with the development of a split personality based on his military days. He almost shoots Datak in the head upon seeing him again, starts using racial slurs against the Votan, slaps Irisa and holds her at gunpoint when she tries to give him Yewll's medicine, ambushes two V.C. guards and nearly kills them under suspicion that they have a chemical weapon (it's just coffee), hallucinates bomb parts in the ambassador's bag, storms into the peace talks with Guns Akimbo, fatally shoots the ambassador when he hallucinates her pulling a gun on him, and almost takes himself and Irisa out in a "blaze of glory" against the vastly outnumbering V.C. forces before Irisa doses him with the medicine. Seeing the hero of the show fall so far in such a short time is chilling. And the worst part is that the split personality hasn't gone away after the medicine dose, and unless Yewll frees herself from Kindzi's control long enough to remove the inflamed Arktech from his brain, he may only get worse.
Kindzi may start a new Dread Harvest, this time adding humans to the menu.
"Of A Demon In My View":
Kindzi using amateur surgery to remove Nolan's Arktech. The way he jerks and spasms around as the knife moves into his skull briefly makes it ambiguous whether he'll even survive.
T'evgin's treatment throughout the episode. He's chained up by Kindzi and has his blood constantly drained to keep him weak. When Nolan finally frees him, he easily overpowers his daughter, but he is then taken by surprise by her false surrender and stabbed in the neck. Finally, just to make sure he won't be getting up again, Kindzi gruesomely disembowels him and eats his heart, gaining his unstoppable power in the process.
The Omec are awake, and the Dread Harvest is about to begin. That would be terrifying in its own right, but in the same scene, we see what Yewll has been doing with her tranquilizing syringes: collecting people from Defiance and imprisoning them in cages for the awakened Omec to feast on. Datak is among them.
The Omec arrived in the next episode, and they are introduced formerly by Kindsi leading them to a chained up Irathient woman to devour ALIVE. We get a very graphic view of her remains, flayed out like a hunting carcass. After that, a Liberata man and a human woman are consumed as well.
Baby Luke, our half human half Castithan baby, is now in immediate danger because Alak was knocked out unconscious trying to save his son. If he was worried about what Rahm Tahk would do to a halfbreed, imagine what Kindzi would do...