1. During Sindel's rampage against the heroes, you get to play as her. and the surviors would be Kabal, Johnny, Soyna, Sub-Zero, Scorpion, and Mileena (explanations down below)
2. Scorpion does indeed spare the Older Sub-zero (Bi-Han) feeling that his family would disapprove of his revenge. Quan Chi is angry, though not wanting to lose Scorpion agrees to let Sub-zero go. Sub-Zero is shocked by this act of mercy and asks Scorpion why, and he answers with a harsh "Don't make me regret it." Having lost in the tournament and humbled he follows Cyrax's example and leaves the Lin Kuei, feeling he cannot return with such a stain on his honor. He ends up joining the heroes for the second tournament and helps Raiden save Smoke however while they are doing that.
3. Sub-Zero the younger's (Kuai Lang) paths follows the same path as in the game, though he is in Outworld attempting to find the heroes and ask what happened to his brother (since he never returned). He gets some misinformation from Quan Chi who tells him Scorpion trapped him in the Netherrealm and attacks Scorpion in Kahn's Stadium. This time, you play as scorpion and beat the younger Sub-Zero. Upon his defeat the Cyborg Lin Kuei take him, (not before offering their services to Kahn in exchange for allowing them to do so). Scorpion ashamed of what he has done, tries to help but Quan Chi stops him. Angered Scorpion fight's Quan and win's and he is let go (Quan Chi leaves whe stadium, but not before we see him give off a mysterious smile.)
4. Where does this lead, well, Noob Siabot is now the corrupted soul of the YOUNGER Sub-Zero, and he controls his original body, now a cyborg, ala original Noob and Cyborg Smoke.
5. The original subby does the whole 'fight with Kintaro and Goro in the clock tower' after Raiden sends him and Nightwolf to investigate what is going on. Scorpion follows (saying that he is doing so as penance for his part in the younger brothers capture) And you get to tag-team between the two against goro and kintaro and later against ermac (who should be made stronger for this fight) and the two are cheered by the captured soldiers.
6. In the graveyard, Sub-Zero meets up with noob and Cyber-zero (and in a very surreal moment both declare that they cast off the bonds of brotherhood towards Subby, saying they are beyond that) and proceed to attack him. He beats both of them saying "brother in exchang for all this you have lost truly something dearly."
7. For Kung Lao chapter, in taking Liu's place he faces a veritable gauntlet consisting of Kano, Reptile, the deadly alliance, Kintaro, Goro( I know what continuity nazi's will say, but it is a great chance for Kung Lao to restore the honor his ancestor lost so long ago.) , then when you think you are facing Kahn next, surprise! you play as Kahn and do a fatality on poor Kung Lao.
8. For Mileena, keep her backstory the same as in the original timeline, and have her track Kitana after he talk with Raiden. As kitana goes along, she fights Jade, then Reptile who is guarding the flesh pits, then she sees all of the clones. Shang comes in and explains but Kitana feels that he should explain to her father and defeats him. Mileena comes in and decides it's time to kill Kitana.
9. Kitana wins, but in their struggle, they open one of the containers whch releases Skarlet (the new character) Her awakening drives her into a rage which forces Kitana and Mileena to work together to stop her. However Skarlet wins and Kahn comes down to see what has happened.
10. impressed with Skarlet's ability he dclairs her to be his new heir and decides to have both Kitana and Mileena executed(explaining Kitana's origins to her to twist the knife and calling Mileena a failed experiment.)
11. While Kitana escapes, we have a chapter with Mileena describing her attempts to reach Skarlet and kill her, proving herself the better clone, however though she reaches skarlet, mileena is defeated once again and hides in the one place no one would expect to find her, among the other clones in the flesh pits. There she witness Kabal's rebirth and seeing his skill against Kano, offer to help him escape the Outworld if he can kill Skarlet. And although he does defeat her, a portal opens and returning reinforcements arrive catch him in the act. Kahn comes in, discovers what's going on and gives Mileena a hard hit with his Wrath Hammer.
12. She flies toward Kabal's direction who uses his new speed to run rings around his foes and heads to the portal. Seeing her, and feeling it's the right thing to do, he carries her out. Mileena is shocked at this turn of events, as Kabal had no reason to rescue her. She is forced to join the forces of light since she has no where else to go. Later during Sindel's rampage against the heroes, Kitana steps in to protect her sister, taking her mother's full wrath (during her death scene when Mileena asks why, kitana says, "We are sisters. is there any other reason?") Also, Stryker is Sindel's final victim (though he does make a brave stand trying to turn himself into a human bomb and tells Kabal to keep up the good work.) and Kabal is next, only for Nightwolf to stand against her.
13. During Jax's chapter we get to see more time with him and Soyna and more of Soyna/Johnny developing. Jax's beatdown of Johnny follows a verbal from him and Raiden about him needing to shape up or ship out (a "reason you suck and you need to fix it" speech) Seeing Jax lose his arms to Ermac while protecting Soyna and himself really drives it home for Johnny, and we see him kick some more ass. And when Jax is up next against Sindel he tells the two "If I don't make it, take care of each other 'lright?")
14. We need to have time with Jax testing out his new arms against Black Dragon goons Kano sent after him and Soyna.
15. Cyrax is the one revived in stead of Cyber-Sub Zero, though since we already played as his human form, we get to see use his self-destruct fatality against Sektor, killing the both of them for good. (Which means no Tekunin in the future.)
16. In the end after Kahn's final defeat Johnny looks around and says "Hey guys, where's Liu?" :o
17. Quan Chi's enslaved souls includes the human Cyrax along side all the other fallen heroes.
18, After the fights in the clocktower, Scorpion notice that Kano has thawed out and escaped.
19. Saddened by the great amount of loss the victory has come with, Raiden leaves announcing that he is relinquishing his position as Earthrealm's protector. (Fujin takes his place in the squeal.)
And that's it. What do you guys think?