The way the dead man in the submarine is framed in the background, and the way the light hitting his eyes almost makes him look like a zombie himself is downright disturbing.
At least you could kill the zombies. Guardians in Among Thieves are fricking Immune to Bullets when you first meet them, and ONE almost kills both you and Tenzin. Then later, after you think you're safe, BAM! They start slaughtering soldiers in the monastery. And once you get used to that, they whip out one of the most powerful and accurate weapons in the game. Much pain and fleeing to heal ensues.
In Uncharted 3, players are treated to spiders. And not just a handful of spiders but entire swarms of thousands upon thousands of potentionally man-eating spiders similar to the creepy crawlies in the first two Mummy films.
They make the bad guys next action to burn down the entire building, quite reasonable.
Uncharted 3 also has hallucinogenic water. When you're hit with this, your entire world becomes blurred, and you live out your worse fears. Not to mention the bad guys can manipulate you into turning against your friends through it.
The sequence where Drake is lost in the Rub' al Khali. Imagine finding oneself stranded in one of the most inhospitable deserts in the world, with no supplies, and no idea where you are going, as you slowly start to weaken from lack of water and the conditions. Drake was lucky he found that village and Salim's tribe when he did.
Pick any MacGuffin from any of the main games and prepare to be horrified at the results. El Dorado? Zombifying anthrax. The Cintamani Stone? A tree full of Psycho Serum. The "djinn" at the heart of Iram of the Pillars? Concentrated Mind Rape. The legendary golden city? Radiated and deadly. Captain Avery's lost treasure and utopia of Libertalia? Nothing wrong with the treasure, but its sheer size and scope caused everyone who knew about it to slaughter each other out of greed and paranoia. Is it any wonder why all of them were sealed away?
Rafe's obsession with Libertalia and proving himself make him dangerous to anyone associated with him. He murders the prison warden in cold blood the second their deal starts going south. He also takes great pleasure in completely dominating Nate in their climatic sword fight, and was only done in when he decided to gloat a little too long. Out of the main villains, he's come the closest to killing Nate. He even gets unique kill animations should the player lose their duel or when Nate gets his Heroic Second Wind: the camera is practically at Nate's eye level and we see Rafe not only slash Nate but stab himwhile Nate is pinned to the ground!
Captain Henry Avery is gradually revealed to be this throughout A Thief's End. Whatever intentions he had when he established Libertalia, by the time he died he'd become a cunning, ruthless overlord driven mad by paranoia and his pursuit of keeping the treasure for himself amidst a pirate rebellion. The island is filled with old gibbets containing the remains of slaves and/or rebel pirates. You can find almost all the bodies of the Libertalia founders seated at a huge banquet table, all of whom were poisoned and left to rot. Some of the late-game areas include a cavern with rooms individually decorated with the skeletal arms, jaws, or rib cages of Avery's enemies. Not whole bodies, just parts. He also mummified dozens of his victims, loaded them with gunpowder, and left them as booby traps. Even Lazarevic never went that far.
The way in which things are shown to have fallen apart is equally unsettling — in every other outing in the series, the lost civilizations Nate finds were destroyed because they went insane from a quasi-supernatural Psycho Serum (zombie plagues, Cintamani sap, hallucinogenic aquifers). Here, Avery and the Founders did what they did only out of simple human greed and cruelty.
In the last chapters of A Thief's End, as you're exploring New Dover with Elena, you can find a note on a table in a gazebo outside one of the flooded mansions that says something along the lines of, "What you take from me, I will also take from you." Floating gently above the gazebo, without being highlighted in any way, is the skeleton of a woman in a tattered blue dress, hung by the neck. It's easy to mistake her for a flag or something, until you happen to look up...