Everyone else was doing it, so I just went with the flow.
Everyone in MK9
With Kahn, Tsung and Sindel all dead, a power struggle outbreaks in Outworld. All of Kahn's former followers are fighting over the throne. Seeing this an oppurtunity to complete his task and kill Raiden, Quan Chi makes his own tournament, the reward being Outworld's throne. The competetors included: Baraka, Mileena, Skarlet, Reptile, Kano, Scorpion and Quan Chi himself. Of course, this wasn't his goal, Chi invited Raiden, Sonya and Johnny to join the tournament. Raiden requested that if Earthrealm won, that all warriors that fought for Earthrealm would be ressurected and that he got to choose Outworld's new ruler. Raiden won the tournanment, foiling Quan Chi's attempts to kill him once more and gained the souls of the fallen Earthrealm warriors. And seeing Kahn's general the best fit to rule, he chose Baraka to be Outworld's new king.
Johnny questions why Raiden would choose the best ruler for Outworld, when he could've ended the entire kingdom right then. Raiden replies that his goal was to get their friends back, and there was no need for more chaos. However, Raiden did question why Quan Chi would even give him a chance to revive his friends, but he does not dwell on the matter and joins in on Earthrealm's celebration.
Meanwhile, Outworld is experiencing even more disruptance after Baraka chose Mileena as his queen. After a quick brawl with Skarlet, Mileena killed her and established dominance as a ruler. However, while Mileena viewed this as an act of romance, Baraka established it as a petty political move, unknowingly breaking Mileena's childish heart and earning himself a new enemy.
Quan Chi finally gives up and breaks his alliance with Shinnok. He seals the deal by ressurecting Shang Tsung and Sindel, officially knocking Baraka off the throne and putting Sindel in his place. Enraged, Shinnok comes out of hiding and sends Reiko to kill Quan Chi, but when that fails, Reiko is sent to kill Raiden instead. Realizing that it's not over after all, Raiden, Liu Kand, and Kung Lao gather up some old friends, Fujin and Kai.
Sub-Zero and Smoke are attacked by Cyrax and Sektor, again hoping to force them into becoming robots. Sub-Zero, finally having a soul again, blatantly refuses and they defeat the two robots before Scorpion challenges them. Scorpion almost kills Smoke, but it ends in a stalemate between Scorpion and Sub-Zero after Scorpion is scolded by Quan-Chi for not waiting for the right time. After Chi and Scorp teleport away, Smoke and Sub-Zero travel back to Earthrealm to treat their wounds.
War finally breaks out when Shinnok attacks Outworld. Shinnok has built an army of undead soldiers using the power Quan Chi gave him before their alliance was broke off. Reptile was the first to attack Shinnok directly in the palace, but dies quickly in battle. The Earthrealm warriors reluctantly intervene, holding back Shinnok's forces. Kitana and Jade attempt to talk to Sindel, but before Sindel and Shang Tsung can kill them, a glass is thrown and shattered at their feet and they are covered by a thick green fog. Before they can react, they are overwhelmed by Tarkatan warriors. A beautiful girl indentified the substance as Tarkata essence, and that it causes Tarkatans to view them as rival males. She says her name is Tanya and leads Kitana and Jade to safety outside the palace.
Sonya, Johnny and Jax are encountered by Ermac. Sonya points out that if they work together, Earthrealm and Outworld could defeat Shinnok. Ermac refuses the offer, saying his allegiance is with Outworld and attacks them. Jax got his revenge for what Ermac did to his arms, but chooses mercy over murder and lets Ermac live. He is encountered by Kenshi after his defeat and prepares for another battle, again facing defeat. However, Kenshi senses Ermac's blind allegiance and attempts to free him from his control. Appearing unsucessful, Ermac defeats Kenshi in another battle, but chooses not to kill him. Kenshi decides that perhaps his attempt worked to some extent.
Kano sees Kitana, Jade and Tanya attempting to escape and tries to stop them. He is stopped in his tracks by Sonya, Jax, and Johnny and is defeated by Sonya who allowed the others to go on ahead. Sonya knocks Kano unconscious and drags him with her, not knowing what to do next. She makes it to the throne room, where Shinnok defeats Scorpion and Quan Chi in battle. Just as he is about to kill Scorpion, Sub-Zero intervenes and freezes Shinnok from the waist down. He quickly breaks free, but not before Scorpion and Sub-Zero escape. He then take one last look at Quan Chi before killing him in cold blood.
As Scorpion and Sub-Zero are about to part ways, Scorpion asks why he was spared. Sub-Zero replies that if Scorpion was to be killed, it was to be by his hand. Scorpion glares and teleports away. The final battle occurs as Raiden, Liu Kang, Fujin, and Kai are all fighting Shinnok. They are, however, unable to overpower him. Shinnok then deals a huge blow by mortally wounding Kai. Enraged, Liu Kang attempts a direct attack, only to be tossed to the side. Shinnok then reveals Quan Chi, in zombie form and under Shinnok's control. This triggers a battle between the four, with Raiden and Fujin coming out victorious.
The story ends as Shang Tsung and Sindel are seen attempting to ressurect Reptile. Mileena is spying on Baraka, vengeance ever-present in her Tarkatan eyes. Kitana, Jade, and Tanya are bonding over sparring and sharing techniques. Raiden is treating Kai's wounds, and asking Fujin to fight alonhside them. Liu Kang and Kung Lao are sparring, with Kang being extremely irritated over his easy defeat. Sonya and Jax are delivering Kano, heavily tied up and disarmed, to helicopter, only for the helicoptor to burst into flames in mid-flight, and Kano parrachuting out at just the right moment. Kenshi is seen worrying over Ermac, and Ermac is seen in deep thought about the murders he's commited. Scorpion is seen in the Netherrealm, wondering about through all the tortured souls, planning his next move. Sub-Zero and Smoke are discussing if Sub made the right decision, and while Smoke says that he should've let him die, Subby strongly disagrees. The game ends as a movie poster comes into view, with Johnny Cage starring in "Defenders of The Realms", his newest blockbuster.
After completing story mode, the player unlocks "Meat Mode", where all the fighters are without skin, you know, like Meat :D
I was asked to go into more detail, so credit to Xperia for Reptile's death detail-
Reptile gathered up the last few surviving members of his race and gave them detailed instructions. He taunts Shinnok as he enters the palace and leads him to a secluded area, allowing the rest of his race to escape unharmed. Shinnok and Reptile have a small skirmish, Reptile almost winning. Realizing he has lost, Reptile activates a cursed item he was carrying and lets it explode in his hand, killing him, but only weakening Shinnok slightly. Khameleon makes a small cameo as she watches in horror as Reptile dies in vain.
Mavado and Nitara have been added to the DLC list.
I know its not the best, but its how I imagine it, so, please comment and constructively criticize! :)