Pretty much the death toll is :
- All the defenders of Earthrealm except Raiden, Sonya and Johnny Cage.
- Shao Kahn, Shang Tsung, Sindel, Motaro (off-screen) for Outworld.
- POSSIBLY Noob for the Netherrealm (seeing as he's a phantom his death may be overrated.)
Meaning, only characters still alive :
1) Raiden
2) Johnny Cage
3) Sonya Blade
4) Sektor
5) Reptile
6) Goro
7) Kintaro
8) Sheeva
9) Mileena
10) Baraka
11) Ermac
12) Quan Chi
13) Scorpion
14) Noob?
---
15) Skarlet
16) Kenshi
17) Rain
* * *
So, here's what I think might happen. I'll warn you some of this shit will be contradictory with itself since we know they'll try to keep a couple of characters around that are currently dead. Also, I might be playing fast and loose with the canon and characters because we know NRS ain't afraid of doing the same.
General Storyline
We know Shinnok's priming himself for an invasion/MK tournament (hey why not declare a MK tournament when you know Earthrealm can only field 3 warriors and you have their own best warriors at your disposal! plus, he can totes rehash the MK2 deal of 1 tournament instead of 10). Shinnok has no reason to accept a tournament unless he gains something substantial about it. So I figure he'd just straight up invade. Instead, it would be Raiden, in a desperate attempt to save time and the maximum amount of lives, that proposes the tournament to Shinnok with the same terms as MK2. Shinnok obviously refuses. Raiden tries to bargain with the souls of all in Earthrealm. Shinnok refuses once more. Raiden is frustrated and does something stupid (because it wouldn't be reboot continuity!Raiden without him doing that) by putting everything he has on the table. If Netherrealm wins, they get the right to merge the realms, all the souls in Earthrealm (obviously, but it's stated just in case nobody caught on) including Raiden's soul, Raiden goes as far as to offer the Elder Gods' Amulet as the grand prize of the tournament to sway Shinnok. He almost bites but Quan Chi dismisses the idea saying they'd just peel it off his corpse anyway. Raiden puts the last condition on the table : Shinnok can participate without being directly challenged but in exchange, Raiden can also participate (wording it in such a way that opens a loophole for Fujin to participate as well). Shinnok guffaws and accepts, as his presence makes the tournament a mere formality. In exchange for all this, Raiden asks for but one thing if Earthrealm wins - the souls of the warriors lost in the Outworld invasion under Quan Chi's thrall. He's not thrilled, but Shinnok puts him in his place.
Why?
This setup does several things - First, you establish why the fuck the game is called Mortal Kombat again in the first place by putting in another tournament. Enough of the stupid shit from DA/Deception onwards. The whole point of the series is the Mortal Kombat tournament and it'd be nice to see the good guys use it to their advantage. This also establishes Raiden as a relatively competent protector of Earthrealm as he does the only logical thing against an invasion of such a massive destructive force. You also restore Raiden's credibility which was severely hurt in the last game.
Sindel fell, everyone died
So what do we do about everyone being dead? Welp, they stay dead for one part. Their story is one of trying to free themselves from Quan Chi and Shinnok's sorcery. They all have different goals, obviously but that's their schtick.
Why?
Death already feels kind of cheap in MK due to all the Fatalities, so it being somewhat serious here since their souls are in the Netherrealm would make for a nice change of pace. Plus, it allows for the interaction between characters that we couldn't really see since they all got fucked up by Sindel hopped up on soul bath salts.
He got Soulnado'd, and he's super mad
What about Noob? I'd say... leave him dead.
"But wait why would Boon kill off the dude he named after himself get off the crack pipe son."
I didn't say he wouldn't come back. Bi-Han never returned to the Netherrealm so if he stays, it shouldn't be as Noob. I'd like it if he was somewhat redeemed (to mirror the fact that he'd no longer be Noob) so we could have a legit Sub-Zero. However, Quan Chi has another Sub-Zero to fuck with. Yes, you know where I'm going.
Bring on Cyber Noob.
Why?
As I said, NRS ain't afraid to fuck with their own canon and they like their role reversals so much that I'd expect something like that. Fucking with the timeline made Smoke stay human and Kuai Liang cybernetized. Why not Zoidberg phantomized? Plus, it'd be another reference to the Noob/Smoke alliance as they'd be rolled into one character. Quan Chi also has another reason to do so since he has Cyrax, who's integration was probably a lot more difficult to handle than Sub-Zero as he allegedly did it willingly as opposed to Sub-Zero. But can you imagine how crazy that'd be? I'd try to play him.
Miscellaneous Stuff :
* Liu Kang's spirit from the original timeline should be Kai (if he comes back)'s spiritual guide. Kai might not know him in this timeline but Liu Kang's spirit would certainly want to give him advice. Especially if Earthrealm's getting hella invaded. Raiden ain't got no time for that shit.
* Shang Tsung should still be a motherfucking snake and manage to escape Shao Kahn's sorcery. Preferably through something convoluted. Here's what I have in mind - Gets absorbed by Sindel through Shao Kahn to power her up. He's technically dead therefore voiding the agreement with Kahn. Sindel gets purified so all the souls powering her up are freed, including Shang Tsung. He's free, he's in Earthrealm, and Quan Chi's soulnado was just dispelled. He discreetly enters the Amulet of Shinnok to bypass detection by all, coming back... I dunno when.
* Scorpion should be the monkey wrench in everyone's plan because he's Scorpion.
I thought way too much about this.
EDIT : Removed Sindel/Nightwolf shit because they're in the Netherrealm.