Remember the Rakghouls? For those who don't, they are mutants that once dwelled in Taris's Undercity, spreading a disease that can turn other people into them when bitten. Unfortunately, the bombing of Taris didn't cause their extinction. In fact, thanks to the bombing, they are almost everywhere on the planet, and their disease has mutated over the past 300 years, rendering the original cure null. Oh, and to make things better, there's a new subspecies of Force-sensitive Rakghouls you have to deal with: Nekghouls.
Better still; some of the things infesting the Selonian tunnels on Corellia are classified as rakghouls. If you take it at face value, then the wretched things have spread from a relative backwater planet, to one of the most important Core worlds. That can't end well.
At one point during the game's first year, there was a one-time event where the disease spread to Tatooine. Then in 2014, the same event repeated on Alderaan, meaning the disease has actually made it to the Core Worlds. Then there's the decontamination procedures taken by each faction if anyone's infected. If Republic, you'll most likely be quarantined and hope the guys from THORN get you cure. If Imperial? Well, off to the incinerator with you! And the epidemic alert in the Imperial space port on Alderaan specifically tells the infected to arrange for their incinerations.
The Kaon Under Siege Flashpoint: A Rakghoul outbreak mutated, causing a Zombie Apocalypse on the planet Kaon. The whole thing is dark and darker, much of it lit by the equivilent of the party's flashlights. You get a desperate cry for help from some mercenaries that are Killed Mid-Sentence, and you go into their camp to find several flavors of zombies, like the Screamer (who is Exactly What It Says on the Tin), the Bloated (who detonate into gobs of oozing green goo) and the Fiend.
In "Rise of the Hutt Cartel", the player is tasked with finding sites where the Seeds of Rage have been buried as part of the GIS quests. These places, and the creatures that inhabit them, do a better job than practically anything else in the game at conveying exactly what Dark Side corruption does to the land. The Seeds aren't doing anything; they're just there, and they still twist their surroundings into a Lovecraftian nightmare.
Oricon. Just when you thought the Dread Masters couldn't possibly be any more horrifying, let's just say what they have planned for three heavily-populated planets - and the excruciating detail they go into to describe it - can induce chills.
The Czerka Core Meltdown Flashpoint tends to run on a nice, big tank of Nightmare Fuel. The party goes into what was once a busy research facility. There are some corpses, a lot of giagntic, nasty droids that shoot everything living on sight, two highly realistic habitat zones with apex predators on the rampage...And when you finally get to the core, you see a handful of surviving scientists imprisoned in the core. To try and shut down the security, you overload the conduits and hear a build-up of energy a split second before there's a busting noise and the scientists scream as they are burned to death by the discharge. Oh, and then you see Vigilant himself, which looks like a cross of a cyborg Rakata and Khem Val, babbling incoherently about blood and death.
The planet of Alderaan. Ignore the breathtaking landscape and rich cultural heritage for a second. Throw them out the window, and just look at the Alderaanian society for what it is: A feudal serfdom state, ruled by noble houses that holds deep seeded hatred for one another, eager to sink their teeth into each other by open warfare and exterminating entire bloodlines. Treaties are negotiated by arranged marriages, and the two superpowers backing their client houses with military support in an attempt to take control of the planet. Resulting in the conflict escalating, while the normal citizens get caught between the crossfire.
One of the worst example was the 'Malevolent Malpractice' bonus objective for Imperial characters during the Alderaan bonus series. In which in addition to raiding an Organa medical camp for medkits, you destroy the kolto tanks there, killing the injured soldiers inside them. Making the entire quest basically a T rated version of the hospital scene in City of Life and Death.
And to make it better, this even extends outside the Jedi Consular storyline. Case in point, Jedi Knight companion character, Kira Carsen.
The sheer number of people who the consular worked and interacted with who later turned out to have a hidden agenda was surprisingly high. To start with, Master Syo, Representative Blaesus, and Ambassador Sophia Farash were all children of the Emperor. Thankfully, at the end of chapter 3, they have all been dealt with, so all is fine, right? Until you play the Imperial Agent's storyline, and discover that Twi'lek Pilgrim Matriarch Kolovish (who was a side quest giver back when you were still a padawan on Tython) and Shuuru, the Selkath representative in the Rift Alliance, were both members of the Star Cabal. The most troubling part was that the consular was said to be one of the most talented Force user in the entire Order. Yet even he/she was unable to notice any signs of things being wrong at all.
In the case of Shuuru, you might even unknowingly give him your endorsement for him to become the Rift Alliance's official representative in the Senate! Which completely undo all the work you have done without ever even realizing it!
Equally as disturbing, the Voice. They are various people who have sacrificed all consciousness to be a public avatar for the Emperor.
The conversation between Pierce and Tanido in this video strongly implies that the Imperial military perform live firing exercises on slaves as part of their training. And worst part is that the two man were joking about it doesn't seem to think that there is anything wrong about that!
Sith Inquisitor Storyline
Khem Val, the Inquisitor's first companion, is very frightening. A Deshade Jedi killer who's lived for thousands of years, his specialty is cutting down Force users and eating them. One of his reminders to the PC is that "[He is] always hungry, little Sith."
When you switch companions, the one leaving usually responds with something along the lines of "I needed a break" or "Call me if you need me". Swap Khem out, and you get this:
Darth Jadus's servants. Not only do they all have a Creepy Monotone, they all look the exact same, and not just because of some character model recycling. Jadus was molding them to his own designs, and they are just as emotionless as he is.
When we learn that he faked his death, he also tortured several Imperial civilians, soldiers and slaves into becoming his mindless servants, some of which you have to kill when you board his dreadnought. The optional ship logs you can come across also give you an idea of what some of the people who got brainwashed were going through before they got broken. We also now know where those creepy servants came from.
The entire concept of Castellan restraints. A secret Imperial project that implants a person with a code word that may be invoked to compel them to obey commands. Imperial Intelligence did this to you, without your knowledge, and a rogue Star Cabal element uses it on you, several times. You have dialogue options to disobey these orders — but they don't work, and you are forced to obey anyway.
Far worse, from a visceral standpoint, is the cutscene that occurs when you realize you have been controlled, and the mental backlash causes you to hallucinate. It begins with your SIS handler morphing into a vision of Darth Jadus on fire and rapid goes into "bad trip" territory before ending in a hallucination (or a recording from those implants you got back when, or a Force ghost or something) of Watcher X, who explains, coldly, what's going on and how utterly helpless you are to prevent it.
The Very Definitely Final Dungeon starts off completely empty, but you soon encounter some relatively simple droid enemies... and then you open another door, and there is a ten feet tall Assimilator droid of a model you've never seen before walking directly towards you in utter silence along a completely empty hallway. Even though the fight itself is a usual SWTOR fare, the first encounter itself is enough to give you a mini-panic attack.