Here is how I would do the film if I were a scriptwriter. I'm assuming that Annihilation is ignored. Also a few of the characters have been simplified or altered slightly for simplicity's sake. All the characters from MK3 would be in it apart from Nightwolf (because I can't think of how to work him in) and Shang Tsung (because he died in the first film). A few characters from MK2 & 4 will also appear. It’s only a pretty rough outline, but tell me what you think:

Opens with Quan-Chi and Kabal talking in an ancient underground complex in Earth. Kabal informs Quan Chi that he has something important to show him and points to Sindel who is walking about the complex. Quan-Chi realizes he can use Sindel’s presence on Earthrealm to allow for Shao Kahn and his invasion force to come to earth to claim her. Kabal demands his reward for he and his ancestor’s supervising Sindel for centuries until she awoke. Quan-Chi “rewards” him by trying to kill him thereby sparing his soul from Shao Kahn. Kabal tries to defend himself, but is killed.

Quan-Chi then goes to Outworld and informs Shao-Kahn that Sindel has been resurrected in Earth after centuries of waiting. Shao-Kahn is delighted and promises Quan-Chi Shang Tsung’s old position.

Shao Kahn goes to Earth and confronts Raiden and co. (essentially the end of the first film). He then takes all the souls in Earth apart from a few that Raiden manages to protect. Raiden tells the others to run and find the help of the other souls he managed to protect. He then attacks Shao Kahn, but is defeated by Kahn and his followers (Motaro, Quan-Chi, Sheeva and Baraka) and captured. Meanwhile Tarkatan warriors attack the others and they must flee. Kitana and Sonya are separated from the others. Sonya is captured by Cyrax who has been lurking nearby undetected. He carries her away from the temple. Johnny Cage and Liu Kang escape and are rejoined by Mileena posing as Kitana. The three of them run as far from the temple as possible.

Cyrax has carried Sonya away from the Tarkatan squads to the Lin Kuei hideout. She is chained up in a room where she sees a bunch of bodies being turned into cyborgs. Among them she sees Jax who has been give cybernetic arms but the rest of him is still fine. He informs her that the Lin Kuei are ninja who have begun modifying themselves to excel in combat. He tells her that some of them, like Cyrax and Sektor, did it voluntarily, while others like Smoke were forced to do it against their will. Cyrax and Sektor are also trying to track down another Lin Kuei who escaped from them.

Meanwhile Johnny Cage, Liu Kang and Mileena are hiding out in a small village unsure what to do. Fujin appears and tells them that he cannot help them directly as he is not guardian of Earthrealm, but he can give them a little help. He tells them how Shao Kahn was able to invade Earth and to stop him they have 2 options. 1: Kill Sindel and Shao Kahn will have no reason to be on Earth and will be sent back to Outworld, but all the souls he stole will not be returned to Earth, or 2:Kill Shao Kahn releasing all the souls he stole and Earth can return to what it was. Fujin then creates a big wind to carry them away from the Tarkatan squads still chasing them to the relative safety of New York City which is deserted and lifeless.

Raiden is meanwhile tied up in Shao Kahn’s base. He has been left guarded by Sheeva and Quan-Chi while Shao Kahn sorts out other matters. While Sheeva is not looking Quan-Chi offers Raiden a deal. If he helps Raiden escape, Raiden will help him defeat Shao Khan. Raiden is torn because he knows Quan-Chi is up to no good, but he agrees reluctantly.

Meanwhile, Sektor and Cyrax are just about to begin experimentation on Sonya when Sub-Zero the younger bursts in and frees Jax and Sonya. The three of them fight their way out of the Lin Kuei base. Jax kills Sektor, Sonya kills Cyrax and Sub Zero is reluctantly forced to kill his old friend Smoke who can no longer recognize him.

Back at Shao Kahn’s base, Raiden and Quan Chi make their move and kill Sheeva. Quan-Chi makes himself scarce after telling Raiden that Shao Kahn has another prisoner. Raiden finds Kitana trapped and releases her. They discover Sindel who is completely under Shao Kahn’s spell. Raiden contemplates killing her and ending the invasion, but Kitana defends her mother and points out that killing her will not restore the souls to Earth. Raiden agrees and teleports them both out of there.

Sonya is busy filling Jax and Sub Zero in on what’s been happening when Raiden and Kitana appear in front of them. Raiden tells them the others are in New York and they must go there now.

Meanwhile in New York, the others are attacked by Barakka and his Tarkatan forces who have chased them using super-powered gliders. During the battle Mileena stabs Johnny Cage in the back and reveals her Tarkatan features. Johnny is saved from the finishing blow by Stryker who was drawn to the battle by the noise. Mileena backs away from Stryker and then Raiden, Sonya, Jax and Sub Zero teleport in. The Tarkatans flee and Baraka is killed by Raiden. Mileena escapes on one of the gliders. Johnny is patched up as best as possible, but it doesn’t look good for him.

Shao Kahn has returned to his base with Motaro to find Raiden and Kitana gone and Sheeva dead. Quan-Chi appears and tells him he doesn’t know what happened only that Sheeva must have made a mistake and allowed Raiden to escape. Motaro is quick to agree with this theory. Just then Mileena enters to tell them that Baraka is dead and the heroes have regrouped in New York. Shao Kahn is outraged at her failure. Sensing her life is in danger, Mileena takes Sindel hostage and threatens to kill her. Quan-Chi uses his magic to free her and then Shao Kahn kills Mileena. Shao Kahn and Quan-Chi then prepare their combined magic to take themselves and Motaro and Sindel to New York to finish this.

They teleport into New York and find the good guys ready. Sub Zero charges into Shao Kahn to avenge his brother who was enslaved by Shang Tsung while trying to assassinate Shao Kahn. Shao Kahn knocks him unconscious with a power bolt. Liu Kang gets ready to take on Shao Kahn, while Sonya, Jax and Stryker prepare to fight Motaro. Raiden and Quan Chi face each other while Kitana faces her mother. Kitana manages to get her mother to fight Shao Kahn’s control. Jax, Sonya and Stryker kill Motaro. Instead of fighting each other, Raiden and Quna Chi turn on Shao Kahn and stun him so that Liu Kang can kill him. All the souls are released and returned to Earth. Unseen by anyone, Quan Chi steals an amulet from Shao Kahn’s body before making himself scarce.

With Earth restored, the heroes separate, and although both a little worse for wear, both Sub Zero and Johnny Cage survive.

The film ends with Quan Chi in the Netherrealm giving the amulet to a mysterious figure (Shinnok) who has plans for Earthrealm.