Well, since the original timeline is over, I decided to use my imagination to figure out what happened in the games that didn't have the technology to give us an in-depth storyline like what we have today. So, here is what I came up with, trying my best to stay as true as I can to the official canon while also taking liberties where I'm allowed and also where I feel it makes sense.

Depending on how this is received, I'll do MK2 and MK3.

Just to be clear, I'm starting off from the beginning of MK2011's story mode, since it's canon up until Raiden has his first flashback. So, here we go:

Sonya: Stand in my way and I'll kick your a--
Shang Tsung: A challenge!?

Raiden, however, had come to put a stop to this nonsense. As a competitor in the tournament, to harass her outside of tournament battle was against the rules of Mortal Kombat. Sonya was forcibly allowed to be let go of, but Jax had to remain. They were on Shang Tsung’s island, and he had complete jurisdiction over who and what came on. Jax was not a competitor and thus was Tsung’s prisoner. Sonya demanded that he be let go of, but there was nothing she or Raiden could do.

As Sonya walked out, Raiden tried to explain to her what was at stake, but she didn’t want to hear about it. Fighting in the contest was the only way to win Jax’s freedom and she wasn’t about to waste her time. Meanwhile, Kano approached Shang Tsung. He was angry about his defeat and he asked if he could challenge Sonya. Tsung decided that he would only be allowed to if he were to aid them in eliminating Earth Realm’s warriors. Kano agreed.

Cage would later approach Raiden and Liu Kang, asking them for help with Sonya’s plight. He wanted to aid her in her mission (probably out of being smitten with her). He thought that her being here may be connected with Raiden’s earlier babbling about the end of the world.

Thus, the tournament commenced!

Scorpion vs. Jade. Scorpion wins. He spares Jade only because he doesn’t want to kill anyone except Sub-Zero. He screams that wherever Sub-Zero is, he’ll kill him for his crimes against his family. Off in the distance, this perplexes Sub-Zero. He never did anything to Scorpion’s family...

Liu Kang vs. Extra Warrior 1. Liu Kang wins. He begs the warrior to concede, but he refuses and keeps at the fight to the end of his life. This bears hard on Kang’s conscience, as this warrior soon had his soul removed.

Sub-Zero vs. Extra Warrior 2. Sub-Zero wins. Sub-Zero kills the warrior. He’s a Lin Kuei, after all. He and Raiden exchange dirty looks (why? The fans know, but we’ll keep that a secret).
Sonya vs. Rain. Sonya wins. Sonya also refuses to kill.
Sektor vs. Extra Warrior 3. Sektor wins. Sektor kills the warrior.

Kitana vs. Nightwolf. Kitana wins. Nightwolf has a keen effect on Kitana, saying he senses much distress inside of her. In the end, Kitana decides to show mercy. There is no need to kill - he has been eliminated. Clearly, there’s more to Kitana than is on the surface. Shang Tsung gets mad.

Cyrax vs. Extra Warrior 5. Cyrax wins. Cyrax kills him.
Cage vs. Ermac. Cage wins. He spares Ermac; he’s not a killer.

Kano vs. Extra Warrior 4. Kano wins. He kills the warrior.

Sheeva vs. Extra Warrior 6. Sheeva wins. Sheeva kills him.

Skarlet vs. Kenshi. Kenshi wins. He spares her. Much like Scorpion, there’s only one person he wants to kill.

Jade tells Kitana later on that she presses her luck too much; she should have killed the Earth warrior. It would show weakness if she didn’t - especially at such a crucial time. Kitana is clearly disturbed about all of this, and tells Jade that she shouldn’t talk since Kitana at least defeated her opponent in the first place.

Following Sonya’s battle, she was approached by Cage, Raiden, and Liu Kang. They sympathized with her and asked if they could assist in any way. After seeing the action that Mortal Kombat had to offer, Sonya decided to trust them. Here was when Raiden instructed them on the legends surrounding Mortal Kombat and what they would be up against. He tells Liu Kang not to be too hung up on his opponent’s death. There would be more to come. Kang isn’t doing well.

Sonya continues to rebuff Cage’s advances (little humor there).

Nightwolf at this point makes himself known to “Haokah” (his people’s name for Raiden). Apparently, they’re quite familiar with each other. Raiden expresses disappointment at his early defeat, and Nightwolf decides he’ll try and make up for it by accompanying them on their journey as something of a spiritual guide. Raiden gives his blessing.

Little did they know they were being watched by Reptile. He reported this alliance to Tsung all that he had seen. Tsung decided to step up his manipulation of the tournament. He calls Sub-Zero, Cyrax, and Sektor...

Raiden approaches the Lin Kuei and tells them he knows what they’re all up to. If they were smart, they would turn away from it all. Sub-Zero rebuffs the thunder god, saying the Lin Kuei never back down from a mission. Raiden expresses disappointment with him, saying that after “his ordeal in the Netherealm”, he thought he would have learned his lesson. Sub-Zero only remains quiet.

The next day commenced:

Liu Kang vs. Cyrax. Cyrax was ordered to kill Liu Kang by Shang Tsung. During the fight, Kang allowed himself to be carried away due to his turmoil and nearly killed Cyrax in the end. He grudgingly allows the assassin to live, knowing deep down it’s the right thing to do.

Johnny Cage vs. Sektor. Sektor was ordered to kill Cage by Shang Tsung. Cage wins, and he spares Sektor.

Sonya vs. Kano. Kano wins. He’s about to kill Sonya, but she concedes defeat at the last moment - not wanting to die at Kano‘s hand. Kano almost kills her anyway, but Raiden interferes.

Sub-Zero vs. Kenshi. Sub-Zero wins. He would have killed Kenshi, but Kenshi concedes defeat - only because he would like to live to see his revenge to fruition. He’ll kill Shang Tsung another time.

Scorpion vs. Sheeva and Kitana. Tsung decides that since Scorpion is otherworldly, two against one would be a more fair fight (he actually only did this to piss Quan Chi off - indeed, Chi gets irked. Tsung is getting in the way of his plan). Scorpion still whips ass, but once again spares the two. He only wants to kill Sub-Zero.
Raiden is very stern with Liu Kang and Sonya’s shortcomings, but Nightwolf intervenes - saying that this isn’t a proper approach. They’re both emotionally fragile at the moment. Sonya runs off in a rage, but Nightwolf is able to talk to Kang. He tells him that if he truly wants to save the Earth, he has to overcome his rage at himself - that the warrior’s death was not really his fault anyway.

Cage meanwhile tries to talk to Sonya, but Sonya lashes out at him. She lost to Kano, and now her chance of getting Jax back is nil. Cage is surprised at how emotional Sonya is...he doesn’t know how to comfort her.

Tsung is glad to see Sonya got eliminated, but he still worries about Johnny Cage and Liu Kang. Meanwhile, he sees no point in keeping Jax around and so he decides to provide the remaining warriors with some entertainment.

Tsung decides to let loose the intimidation. He wants them all to see Goro. The warriors get their first glimpse of him, and to demonstrate his strength, Jax is put in a ring with him. Raiden can’t do anything - Jax is Tsung’s property on his island, not a competitor. He’s seen this many times before. Despite Jax’s best efforts, Goro beats him down. Goro is about to kill Jax in the end, but Liu Kang intervenes. He declares this to be unruly...and that he’ll volunteer to be Goro’s victim when they meet in the final battle. Goro is stunned by Kang’s audacity and due to this show of comradeship appealing to his Shokan honor, he decides to spare Jax. This makes Shang Tsung very angry.

This act of selflessness also makes an impression on Kitana.

But it wasn't totally an act of selflessness. Liu Kang did it partly because he had hoped he would die, his guilt eating his fragile personality aside (he is, after all, a peaceful Shaolin monk). Raiden realizes this and chastises his selfishness. Kang is left confused and bitter.

Jax is reunited with Sonya. His wounds are tended to by Nightwolf and Raiden.

Cyrax and Sektor, now eliminated, feel like doing Sub-Zero a favor out of Lin Kuei brotherhood and sneak up on Scorpion. Scorpion beats the both of them up, leaving them behind as a message to Sub-Zero.

Next day, the tournament is ongoing...

Liu Kang vs. Cage and Kano. Tsung set it up this way to make the fight extremely difficult for Kang, who continues to advance. The battle takes place on The Pit. The fight is rather complex, and at one point Kano incapacitates Kang, leaving the fight between him and Cage. Cage manages to knock Kano off of the pit...leading some to think he’s dead. Kang returns and he and Cage decide to fight it out to see who gets to face Goro. In the end, Kang wins. Cage gratefully concedes. By defeating Cage, Kang realizes that what has to be done has to be done. He washes his guilt away.

Sub-Zero vs. Scorpion. Tsung decided that he would save Sub-Zero for whoever came out on top in the other fight - he was, after all, the sole of his warriors to advance this far and Kano would pretty much be dead weight cast off in the other fight (he wasn‘t really needed anymore anyway - one more Earth warrior down). So, he decided to give Scorpion his fight. Scorpion wins. He takes his revenge on Sub-Zero, killing him...despite Sub-Zero’s constant pleas that he did not kill Scorpion’s family.

As Cage’s injuries are tended to, Sonya doesn’t know whether to be angry or touched with Cage’s actions. She chastises him, saying that he stole away her chance for his apprehension. Still, she offers a small ounce of gratitude when Cage tells her he did it partly for her honor. Still, Sonya can’t help but feel agitated.

Tsung is very unhappy with the results of both fights. He sends Kitana to kill Liu Kang and end this once and for all.

Kitana makes her advance, but Kang manages to beat her down. Kitana demands to be killed, having failed her ‘father’ again. Kang refuses to kill her, telling her that she should reconsider the way that she lives...leaving Kitana with very confused thoughts. Kang doesn’t realize how much he affected her as she leaves.

Kitana lies to Shang Tsung and says that Raiden interfered before she could get her chance.

The final fight of the tournament before the championship: Liu Kang vs. Scorpion. Quan Chi appears to taunt Shang Tsung about Scorpion’s possible victory. He doesn’t care how Mortal Kombat ends with if neither an Earth or Outworld warrior take the title. He says that he will get what he has come for (whatever that is). Tsung angrily brushes him off.

On the eve of the fight, all of a sudden a Masked Guard appears. He demands to challenge Kang for the right to face Goro himself! Tsung is very unamused and sends Baraka after him. The Masked Guard reveals himself to be Kung Lao, a monk from Liu Kang’s temple! The two fight briefly, with Baraka coming out on top. Baraka would have killed Lao, but Raiden interfered. He justified his actions, saying that he could step in since the battle was outside of tournament regulations.

Kung Lao gets lectured and humbled by Raiden right after. They all watch as Liu Kang takes on Scorpion. Kang manages to win.

Scorpion regrets his loss, but tells Quan Chi as far as he is concerned the battle was won. Sub-Zero is dead. Quan Chi replies nonchalantly, saying that they got what they came for anyway (once again - mystery). They head to the Netherealm.

Kang has advanced the furthest. Now, he awaits Goro...Kang is dropped to his lair. The two of them exchange honorable ethics, and then prepare for battle. Kang fights hard and at some point it seems as though he will lose. When he begins to gain the upper hand, though, Goro lashes out in fury - abandoning his ethic in favor of pride. In the process, he begins to destroy everything around him. Kang merely dodges and avoids, knowing Goro is pretty much just hurting himself. Goro destroys too much and eventually a wall caves on him. The rubble completely buries his body. Kang can only offer a heartfelt bow - he does seem genuinely sad about this - but he has won Mortal Kombat.

Shang Tsung is furious. He challenges Liu Kang, as he had stated at the beginning. The two of them fight and in the end, Kang manages to win. Though Tsung demands death, Kang merely tells him to concede. He does. The Earth has won.

The remaining Outworld warriors - Shang Tsung, Jade, Baraka, Reptile, Rain, Kitana, Ermac, Sheeva, and Skarlet - all return to their emperor, dreading the news they’re about to relay. Kitana takes one last look at Kang before entering the portal. This man has really changed her life.

Raiden creates a portal back to Earth, and he puts Liu Kang, Kung Lao, Johnny Cage, Sonya Blade, Jax Briggs, Nightwolf, Kenshi, Cyrax, and Sektor through it. Nightwolf and Kenshi express their respect for Liu Kang and then take their leave (Kenshi cryptically tells Kang he’s glad he didn’t kill Tsung). As for Cyrax and Sektor, they run for it immediately...completely flabbergasted with what they just experienced.

Kang, Lao, Cage, Sonya, and Jax decide to head to the Wu Shi Academy.