The Pit II's stage fatality, more frightening than the first. Your character uppercuts the opponent off of a bridge from a tall height, and then the view the player is given transitions from the usual side-on view to a top-down view of the victim flailing their arms about while accelerating towards the ground, then shattering their spines with a loud "CRUNCH!" when they hit the jagged rocks below.
Scorpion's "breathing fire at his opponent" fatality as portrayed in this game. When he performs the fatality and his opponent is reduced to a pile of bones on the ground/floor, said bones are still glowing from whatever is left of the fire.
Baraka is a creepy-looking character, especially when he does his Mortal Kombat II victory pose when he turns to the screen, bows his head and looks up at the screen.
Mileena. Body of an intoxicatingly beautiful woman, jaws like a bear trap, skills of a deadly warrior. Plus, add in her insane, almost childlike personality and you have one of the most chilling (and popular) characters in the Mortal Kombat series.
This game had a special type of grab called "Bone Breakers", which meant grabbing an opponent's limb and cracking it at the elbow or knee (with the knee being especially gruesome by bending the opponent's knee backwards). Sickening Crunch obligatory, obviously.
His Possession fatality, later inherited by Shang Tsung. He becomes a light, enters your body, and forces you to rip off your own head, revealing his own head under it.
Even worse, doing this on Shujinko, depending on the console, will wield one of two occurrences. On the PS2, PSP, and GameCube versions, after Liu Kang forces Shujinko to rip off his own head, Liu Kang's own head does not appear. On the Xbox version, the moment he rips off his head, the game freezes with a sudden, loud buzzing noise that is actually quite common for the console in general when it experiences errors like this.
Dark Raiden. The caring and compassionate thunder god of the past is gone and has been replaced by a merciless and cold-hearted jerkass who is quickly growing tired of humanity.
Havik, to some extent. Take his 'Human Pencil Sharpener' fatality. It's bad enough to have a dude with a skull face eating your arms, but then to puke up your blood afterwards is just awful! See for yourself.
In the recreation of the Living Forest from MK2, it's possible to throw your enemies to the trees. They can also throw you in order to be eaten alive by those trees if your opponents do the stage fatality on you - and there are corpses hanging from the branches... which struggle to get free, and then abruptly slacken!