Near the very end when :you're out of the animus and you suddenly gain Alta´r's Eagle Vision, it is surprisingly disturbing when playing for the first time, and everything goes film negative, with glowing red symbols and cryptic passages scrawled all over the walls and floor. Especially when you realize what some of those symbols are... This gets even more chilling, however, when you go into the bedroom and find phrases in quite readable English saying things like "I have entered the Abyss and never returned." Of course, this entire time these things have been written above your bed, where you have been sleeping for the last several days. Few things are scarier than the sudden ability to see invisible things that were right next to you all along. And then there are the implications that all the unusual writings are from the previous "subject", who wrote them with his blood.
Once you figure out what the seemingly-random letters in the main room say. Specifically, the triangle: "THEY DRAINED MY SOUL AND MADE IT THEIRS I DRAINED MY BODY TO SHOW YOU WHERE I SAW IT"?
When you go to confront Al Mualim. Hundreds of brainwashed people telling you how wonderful Al Mualim is, all the while walking straight towards you. They don't attack you, they don't even chase you, they just follow you. So subtle, so harmless, and yet so very, very creepy.
Which can also double a Fridge Brilliance, since what Al Mualim did with Masyaf is exactly what Abstergo plans to do with the whole planet. What better way to motivate the player to defeat the Templars than to give the player a taste of what to expect if the Templars win?
All of Alta´r's targets: powerhungry, ruthless, and completely amoral people who are ready to take over the Holy Lands with any means possible. All of their first appearances have them Kick the Dog both brutally and terrifying, such as Garnier orders his guards to break a escaped "patient's" legs just to make sure he doesn't run away again, Abu'l poisoning his guests with poisoned wine and then lets his archers have their ways, Jubair burns one of his own followers to death because he critiqued his book burning. And then comes Majd Addin, a sadistic regent lord who personally executes "enemies of the state" for fun, Sibrand, a guy who has gone so insane with fear of death that he'll not just kill scholars on the open street but also tries to shoot birds because he thinks they're assassins as he's too insane to see the differences, Garnier's "hospital" and the "patients" inside, Talal's underground headquarter which's filled with kidnapped people begging you for help from their cages and you can't do nothing to help them. The actually scary part? They think they're doing good. They think they make a better world through their ways. They're so fanatical in their beliefs that they simply refuse to see that they actually make things worse than they are. Even when dying in Alta´r's arms, they continue to claim they've done nothing wrong except dying too early to make any actual "difference".
The first thing you see in the game is a group of beautiful women, following you very closely. They don't have faces, and neither does anyone in the marketplace that you are suddenly teleported to.
The Pieces of Eden often have horrific effects on their users. The Codex written by Alta´r vaguely hints at this by his flip-flopping between succumbing to the Apple's temptations and gifts of knowledge, and a reluctance to ever touch it again for fear of what it could do. The Shroud heals wounds... if it doesn't inflict Mind Rape or Body Horror on you (but both is more likely).