Ever played a game that is otherwise far from scary and at some point it gets into an atmospheric or horror segment in the story that makes you go: "what the hell happened here!?"

It could be a non-scary game taking you to a place where there is:

1) Horror scene

2) Eerie, hunted place

3) Brutal death story segment/tragedy

4) Violent episode

5) etc.

Anything that of the sort that comes to your mind? How did that scene make you feel?

Majora's Mask had plenty of that. While it's a Zelda game, it was a bizarre game overall with heavy atmophere, some dark areas, and monsters that looked much worse than the normal for Zelda games. The music also helped setting the tone... some parts were really macabre, like the whole Ikana Canyon and its mummies/ghosts/creepy stories.

Uncharted 1 and 2 near the end when the monsters pop up. Especially in 1, where it reminds me a lot about one of the scariest films of all-time - the descent!

i was going to say the same thing about uncharted drakes fortune. the descendants are quite scary and one of my favorite parts of the game.

Metroid Prime 2 Echoes
The entire game.

Zelda skyward sword... those freaking trials at the end to power up the sword were scary as hell.

lol it's already been said but Majora's Mask definitely fits that game that's cheery on the surface but so creepy otherwise.

This really doesn't fit too well, but I remember an experience from Warcraft. There was this troll woman in Outlands who seemed to run a nursery or something, she had all these babies around her out in the middle of nowhere. Later in Warlords you find out she's there in the past, but she's not a troll (forget what she was) and instead learn she's been stealing the lives of others to continue living indefinitely. Really made that seemingly sweet nursery from years later really look like something else entirely lol

ummm... Earthbound has plenty of that atmosphere. I'm not coming up with as many examples as I thought I would.

Epic Mickey

EarthBound

Super Paper Mario (That river with the hands and really creepy music)

Ocarina of Time (The Well, Shadow Temple)

Psychonauts (Secret room in Milla's mind, the asylum)

Pokémon Platinum (Old Chateau)

Pokémon Gold (The Union Cave music creeped me out as a kid, it's not actually scary though)

Donkey Kong 64 (Frantic Factory)

Super Mario 64 (Haunted House, especially that freaking piano!)

There are probably more, but I don't remember right now. If I remember later I'll edit my post.

EDIT: I'm starting to see a pattern here, why does Nintendo put so many creepy things in their games? lol