Sub-Zero? After defeating Scorpion (his brother's killer), the Cyber Lin Kuei interrupt and haul Subby back to be used in the Cyber Initiative, much like Smoke was in the original timeline. He manages to have his free will restored and is wracked with guilt over all of the actions he had no control of. Upon attempting to stop Quan Chi from creating a Soulnado, he's blocked by Noob Saibot, who reveals himself to be Sub-Zero's elder brother (compare this to the first timeline, where Sub-Zero didn't discover this fact until Deception). Noob then kicks the dog by telling his little brother (the very same one who idolized him and entered the Outworld tournament to avenge his death) "We share blood. We are not brothers." Later, Cyber Sub-Zero is killed by Sindel. Even worse, his ending (as Cyb-Zero) has him defeating Shao Kahn, only for Kahn's soul to commit Grand Theft Me on him.
Scorpion? Scorpion continues to demand that Shang Tsung allow him to fight Sub-Zero, who Scorpion believes to be the killer of his family and clan. After fighting multiple pawns and demanding Sub-Zero, Scorpion is promptly denied and is approached by Raiden. Raiden says he will ask the Elder Gods to revive all Scorpion has lost if he doesn't kill Sub-Zero, believing Sub-Zero to be part of the prophecy. When Sub-Zero finally does fight Scorpion, Scorpion defeats him and doesn't kill him. Only after Quan Chi shows Scorpion terrifyingly graphic images of his family and clan being killed by Sub-Zero does Scorpion finally give in and kill him, overtaken by anger. This leads to the elder Sub-Zero's resurrection as Noob Saibot. The worst part? It wasn't even Sub-Zero who murdered Scorpion's wife, child, and the rest of the Shirai Ryu; it was Quan Chi in disguise.
Oh, it goes more than that. Sindel, that person who commits those mass murder to nearly everyone? It wasn't her idea to do it. It was Shao Kahn imbuing her with Shang Tsung and his many souls when all she suggests was just "taking on the battlefield." Things went out of control from that point on, since if her Arcade ending is to be trusted, if it wasn't for being imbued with Shang Tsung's souls, Sindel would return to her noble self. Did death by Nightwolf set her free? Nope. She's doomed to be Quan Chi's undead slave along with the people she killed for things that was out of her own control (and if they ever regain sentience, they'll certainly blame her for their fate). And the fandom hates her for it and think she was a mass-murdering harpy all along.
If there's anyone who has it worse than Raiden, it's Liu Kang. He grows increasingly intolerant of Raiden's visions. He then watches as Shao Kahn snaps the neck of his stalwart companion Kung Lao and later sees his lover Kitana die mere seconds after he and Raiden return from their meeting with the Elder Gods. This is the straw that breaks the camel's back, and Liu Kang calls out his mentor forthe futility of the other heroes' sacrifices, believing Raiden to have gone mad. His faith in the Thunder God shattered, Liu Kang attempts to fight Shao Kahn, only to be stopped by Raiden. A fight ensues, culminating with Raiden accidentally frying Liu Kang in self-defense. As Raiden grieves, Liu Kang curses him with his dying breath and says, "You have doomed us all."Poor Liu.