Simply amazing.
This is exactly how I would imagine a sequel to MK9 to be like if it were produced by NetherRealm Studios. Your elaborations and fleshing out of details during the events of MK4, simultaneously considering the changes done to the timeline by Raiden are perfectly aligned with NRS' style of story telling. While I have small doubts that some of these characters and story concepts would be incorporated, such as Shujinko (how would they find him?) or Red Dragon's Human-Dragon hybrids, they are very welcomed and you introduce them in a sound manner. The liberties you take with the story, such as Shinnok's shrines and the soul tower granting him even more power, again, simply awesome and very logical. While some people raise doubts that MK11 would be a lot like MK4, which I think your story is (and I don't mean that in a bad way, since MK9 was after all a re-telling of MK1-3 on the most part), I really enjoyed how you fleshed it out and made it MK4 with some minor changes like Liu Kang being destined to defeat Shinnok or Scorpion destined to discover Quan Chi's treachery. The subtle connections to original concepts if very interesting as well; Corrupt Raiden and demonic Lin Kuei cyborgs comes to mind. Making Mileena do a complete flip on her character from MK9 was smart and is cleverly connected with her MK9 arcade ending, though I was of the impression she would be irredeemably evil in this new timeline, I guess there is room otherwise thanks to bother her own arcade ending implying she was in fact influenced by sorcery and Kitana's arcade ending; I'm not sure if this was intentional, but it also seemed that you transformed her character as a reference to how she was originally portrayed before MK9 which is pretty clever as well.
Random things I liked in particular:
- The including of the Red Dragon and Mavado.
- Fuijin becoming Earth's protector as originally intended.
- All the enemy factions created; really brought a sense of dread and sounded overwhelming compared to worn down forces of Light.
- Lin Kuei strategically eliminating world leaders.
- Kano defeating Sonya for a moment in a reverse of irony.
- Everyone had a role in the story.
- Shinnok's role in the story as a cunning, powerful and menacing antagonist makes an impression comparable and unique alongside Shao Kahn.
- Liu Kang's perception being entirely deluded, but is managed to be saved by Nightwolf.
- Liu Kang's fatality on Shinnok.
- All the heroes are wished back by Liu Kang's request.
- Shang Tsung's return; his luck never seems to run out.
- Kano saves Kabal yet again. Guess this implies Kabal is destined to returned to the Black Dragon, isn't he?
I guess the main problem with this is like you said with the chapter format like they did in MK9, but who says it will be like this? MK9 deviated from it when Kung Lao died to Shao Kahn. I imagine a lot of this could still be organised mostly in this manner, though. As for someone else being a host for Onaga, I don't think he will take any form that isn't like his Dragon state we seen in MK: Deception. He is called the "Dragon" king, after all; I believe his design was intentional, even if it deviated from his initial appearance in Raiden's Deadly Alliance ending and will probably stay that way.
This story really makes me want to see you write a fan fiction fleshing out the original timeline and even a sequel to this.
Question: Does your story interpret Noob Saibot's death in MK9 to just be temporary?
Overall, I am immensely impressed.