Not to mention the game is between MKII and MKIII

Here's what I'm thinking and if I am right I get a cookie, Now this is purely speculation but I think the plot will involve a lot of betrayal and plot twists coming from both ends.

The big mystery of the game would be the reason as to why the two realms are merged together. Portals would mysteriously open in both Gotham and Metropolis. In Gotham, Batman would encounter the Joker who escaped from Arkham and is expected to have foul-play. Batman would encounter Joker in a conflict and somehow both of them would be caught in a vortex that transports Batman and Joker to seperate parts of the MK Universe. In the void Joker was swept away to Outworld in the MK Universe, and Batman to Earthrealm. The story would start off with Batman as the first character you play as if you choose the DC side, and on the MK Side Sub-Zero.

This would my prolouge to the storymode.

I would have Batman wind up in the polar regions of Earthrealm where the Lin Kuei temple is located. Batman would do some scouting in the region and would be attacked by a yeti (the white monsters in Armaggedon) Batman would struggle with the beast but would manage to take it down. Weakened by that encounter, Batman would be ambushed by a group of Lin Kuei and knocked unconcious. Batman would awaken in the Lin Kuei temple and he would lockpick his bindings and attempt to escape. Batman would easily dispatch any Lin Kuei that would get in his way and make his way to exiting the Lin Kuei Temple. Batman would make his way to Sub-Zero's chambers and encounter Sub-Zero himself. The two would struggle and Batman would be incarcarated by Sub-Zero's ice blast. Batman would be constricted once again and be interogatted by Sub-Zero

Batman would evaluate Sub-Zero and his Lin Kuei after being interogated and he would point out their weaknesses. Sub-Zero would view Batman as a threat to his clan with his resoursfulness and would decide to keep Batman imprisoned. Batman would eventually escape again and this time be succesful. Sub-Zero would be alerted to this news and would seek out the aid of Raiden to question the thunder god on the information he gained from Batman

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In another part of Earthrealm Jax and Sonya would be investigating a disturbance in their inter-realm equipment due to a portal opening that is causing a jamming in their devices. Sonya would lead a team of Outerworld Agents to investigate the disturbance. Jax back at base would monitor Sonya's progress as well as keep check of the data on the equipment. However, this routine check would go terribly wrong. When Sonya arrived on the scene to investigate the portal she was completley caught off guard due to a bomb detonating when her team arrived. Sonya was presumed dead by Jax as her radio was cut off from the explosion. However, as if on cue Jax's base was ambushed by none other than Deathstroke who mowed down Jax's men with gun shots and slashes of his sword. Jax and Deathstroke confronted each other and their fight was interrupted when Jax's equipment was destroyed by carefully planted bombs by Deathstroke. During the chaos Deathstroke escaped and Jax managed to leave the ordeal with his life intact.
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Due to this being a long post i'm going to take a break and ramble on about my theories, Hopefully you guys enjoy the pointless time I put in to writing this, because honestly I had nothing better today while at work lol.

katana im your fan

Jack Burton is impressed with Grizzle's prologue...

I wouldn't be surprised to see situations like that in the game.

It is not between MKII and MK3, even though it's been explicitly described as borrowing design and sensibility from that period. It is removed from completely definitive connections to the core MK series.
It is an alternate universe. A side game. A spin-off.

http://secretearths.blogspot.com/2008/09/mortal-kombatdc-universe-hans-lo.html