When Ed Boon said that this would be the bloodiest MK game of the series, he wasn't making stuff up. What he didn't tell us is that most of it would give us horrible nightmares.
The intro sequence of the Story Mode. Every single character that appeared in the series until Armageddon is dead and in bloody chunks save for Shao Kahn and Raiden, the former beating the ever-loving crap out of the latter while delivering a chilling "The Reason You Suck" Speech... And to get into more detail, just to see how scary it is: dead bodies everywhere; vultures eating Sonya's severed body, Johnny Cage's head, Baraka cut in half by Kung Lao's razor hat, you name it.
The fate of all but two of the members of the Forces of Light. Raiden's failure to successfully interpret the visions of his future self led him to make mistake after mistake, each one more costly than the last. Nine of the heroes died in the battle against Sindel, and all of them are now slaves of Quan Chi. Liu Kang, the most devout of the group, loses his faith in Raiden and is accidentally killed by him. And after everything's said and done, all that's left for the final fight are Johnny Cage and Sonya...
Shang Tsung's demise: Shao Kahn basically absorbs Shang into himself, much like when Shang steals a soul. Talk about Irony.
The X-Ray combos, showing bones snapping like twigs and organs pulsating.
Sub-Zero's X-ray combo is especially horrifying: he plunges his hand into the victim's side, freezes their liver, and crushes it.
Goro's X-ray move deserves special mention. He lifts up his opponent and squeezes their head so hard that their skull cracks, exposing some of the brain. This is then followed by a one-handed toss to the ground, which breaks the skull and neck even further.
Quan Chi's X-ray takes People Puppets and refines it to a horrific extent. He controls them with his amulet and tosses them a skull, which they proceed to ram against their skull and crack it. After that, he forces them to snap their own neck.
Baraka, Kitana, Reptile, and Skarlet all give the opponent an Eye Scream.
Baraka uses one of his blades to lift the opponent and stab them through their neck and then one of their eyes.
Kitana warps behind the opponent and sticks her fans in the back of their skull, then warps in front of them and removes the fans only to put them through the eyes
Reptile sticks his claws through the eyes and snaps the neck before kicking them away.
Skarlet slams her palm into their face before sticking one of her high heels into an eye.
One that truly stands out is Noob Saibot's "Make a Wish". He summons his shadow clone on the opposite side of the opponent. Both he and the clone grab onto one of the opponent's legs and pull, slowly ripping the opponent in half vertically, with the opponent still alive throughout the entire thing until their body splits completely.
And then there's his second Fatality, "As One". He summons his shadow clone, which drags his opponent down into a portal and then closes it shut on their waist, severing them in two. The character in question then agonizingly crawls to their death after Saibot, with blood spewing from where their legs used to be.
Shang Tsung's "Possession" fatality: he turns himself into a mist form and flies inside the opponent, leaving them confused. It appears to do nothing until their eyes glow green and their hand starts moving on its own, reaching for their head. They try to push it away, but cannot. As their hand grabs onto their head, they let out a horrified "No!" before ripping it off themselves. Shang then flies out of the body and lets out an Evil Laugh.
Skarlet's "Blood Bath" fatality is particularly horrific; not only does she slit your throat, but she tilts your head back and lets your blood spray on her.
Her second fatality, "Make It Rain", is even more terrifying. She stabs herself and melts into a puddle of blood that slithers underneath the opponent. Then, four spikes made of hardened blood come out of the puddle, impaling the opponent through their arms and legs and lifting them above her, who emerges shortly after. She then proceeds to cut the opponent open and lets the blood rain down on her.
Scorpion's "Nether-Gate" fatality consists of him stabbing his opponent in the chest with his spear and wrapping the chain around them, then kicking them into a portal to the Netherrealm that flays them alive. Their skeleton drops out of another portal, still hanging from the chain.
The Klassic Skins DLC also includes his classic "Toasty!" fatality, rendered in all of its 3D glory and horror.
Sheeva's "Stripped Down" fatality is now rendered in all of its horrifically bloody HD glory.
Smoke's "Smoked Out" involves Smoke plugging his fingers into his opponent's cranium and then removing them, where his smoke then melts his foe like acid from the inside out. The player is greeted by the hapless victim screaming in pain as their skin and most of their muscle tissue is burned away.
His second fatality, "Tremor", involves him doing his smoke teleport through the opponent. The victim barely gets time to scream before they fall apart into a heap.
Nightwolf's "Ascension" fatality consists of sending the skin of his defeated opponent to Heaven. Just the skin.
Rain's first fatality, "Bubble Burst", is absolutely horrific. He creates a large bubble of water over his opponent's head which forces itself down into their mouth, causing them to expand to terrifying proportions...then they explode.
Even the bosses have fatalities, and they're just as scary as the others:
Goro can either tear your head off and rip it into fourths, or dismember you before tearing your body in half lengthwise.
Kintaro can either rip off your arms and head (and rip the head in half, as well), or quarter you with his bare hands.
But Shao Kahn tops them all: he either tosses you in the air and smashes you to bits with one swipe of his hammer, or plunges his bare hands into your chest and tears you in half like he was parting a curtain.
While the Krypt is usually a disturbing place in most of the games, it generally is not bad enough to warrant any scares. Mortal Kombat 9 breaks this tradition by including a random screamer in it. Emphasis on random.
The stage fatalities.
In the Street, you are thrown in front of a taxi and get decapitated on impact with its bumper. The twisted body you leave behind looks even worse.
In Scorpion's Lair, your face is burned off by lava, which pours out of your open mouth before your skull is kicked under again.
In the Subway, your head is repeatedly slammed against a passing train and then thrown in front of another one.
Kratos' Arena has an option to do THREE different death traps: crushing, burning alive and being sliced into pieces.
Remember how Shaolin Monks was the first time you could actually feed your enemies to the trees in The Living Forest? Yeah, that's back. The victor tosses their dazed opponent into the maw of a hungry tree that proceeds to chew away, eventually biting off the legs and swallowing the torso. As the camera zooms out, the legs are still twitching.
The worst by far is Kabal, whose mask can be knocked off, (something which should kill him, but we can see the breathing hose is connected to his throat) revealing just how gruesome a toll the experience of being burned alive by Kintaro can take on your appearance.
Speaking of which, said experience is scary on its own: in Chapter 12, after witnessing Raiden's killing of Motaro, Kintaro appears in front of both Stryker and him and proceeds to roast the latter.
Special mention goes to Cyber Sub-Zero, whose brain gets exposed. This also happens to the Retro Cyber-Ninjas and Sektor's default if you look closely.
The DLC character Skarlet. The concept of a warrior made from the blood of fallen warriors and capable of manipulating blood is quite frightening.
If, with everything mentioned above, MK9 wasn't nightmare-inducing enough, the fact that Freddy Krueger himself is a Guest Fighter totally seals the deal.
That being said, his fatalities are no slouches either:
In the first one, he summons a boiler out of the ground, and then tosses the conquered foe in it. They start burning to death; not immediately like Scorpion's "Toasty!" fatality, slowly. They try to stumble out, but all they can do is get one of their arms out of it, and Freddy slams the boiler door on the grasping appendage, severing it.
Reptile's arcade ending: after he kills Shao Kahn, he finally manages thanks to Shang Tsung to restore his race...then he leads them into a genocidal rampage against tarkatas, shokan and centaurians, complete with the shot of Reptile burning a tarkata child's face off with acid puke. it's not just the sheer brutality of this ending, but the fact that in a series choke-full of Humanoid Abominations, Reptile was the closest thing to an Anti-Villain, discovering he could be capable of such gratuitous and ruthless cruelty makes everything worse. he gloriously jumped the slippery slope.
Kitana's perspective of Sindel's role in the story has to be this on a personal level. First the Princess sees her mother again for the first time since awakening to the truth about her past and her family. However, this is as far from a happy reunion as you can get. The first thing her mother does is unleash a terrible sonic scream while casually walking towards her and her allies and proceed to challenge them all to a fight to the death. In a terrifying display of power and brutality, Sindel proceeds to completely wipe the floor with ten of the 64 purportedly greatest fighters in all the realms, viciously killing six of them in the process, before subjecting Kitana to a merciless beating at the hands of her own gleefully grinning and laughing mother. As Kitana pleads for mother to remember Edenia, she is cruelly disowned as a traitor to Shao Kahn, leaving her heartbroken on top of being powerless to stop her mother from ripping out and absorbing her soul. To make things worse, her soul may or may not have heard Nightwolf get up and call her mother a monster towards the end of the absorption.