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.
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. Ot try and shut down the security, you overloadthe 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.
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."
Bounty Hunter Storyline
Imperial Agent Storyline
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.