Batman will knock some sense into Superman(eventually)
Superman will then fly around the earth so many times that he'll rewind time. He'll then prevent all this from ever happening........again.
The End ;)

Possibly quite a few characters may die who knows but I do still want to know how the heck can someone like joker take on superman in this game hope there's a good explanation for that

Thanks for typing all that I was about to type the same thing. Great minds think alike

The heroes find out Ares, God of War, manipulated them, engineered the whole Joker-blows-up-Metropolis thing, maybe even somehow messed with some of the "Regime" members' minds to make them more susceptible to certain out-of-character dictatorial behavior, all to plunge the world into a superhuman war, and they put aside their differences to take him down.

Batman and Superman kill eachother, then Quan Chi reveals himself with the amulet.

Scarecrow comes out in the final fight and sings the Trolol song that he laced everyone with his toxin and Batman, as usual, was immune to it and eats the Hay-ll out of him.

Or an altrnate ending, Batman beats up the JLA and makes them sit down in an IMAX theater and plays the finale of JLDoom and on this rare ocassion, Batman LOL's like in the BatmanTAS episode when Harley has him having in the Piranha tank with big fat "I told you so"

I feel as though you deserve a Dragon Point for this, sir!

Right to explain I'm just going to go through what I think happens in story mode.

Firstly Justice League are together on the Regime thing.

Batman is the first to turn not liking the whole thing. Joins up with Green Arrow, Catwoman, Harley and resurrects Grundy to form Team Gotham.

Green Lantern next to turn because Superman is breeching Green Lantern laws or something. I dont know GL that much but they are basically space police yeah?

Flash and Shazam next to turn not too long after the takeover of Atlantis.

Other heroes turn on Superman but are afraid to actively oppose him.

Wonder Woman is the last to turn because she always been seen as a bit law forceful. Superman starts fucking with Thymiscyra and that shit dont fly with Wondie.

A pact is formed between everyone for one last attack on Big Daddy Superman.

A false war Between The Amazons and Atlanteans designed to distract him momentairly. (Turns out to be a major dick move) Lex n Bane frees Doomsday.

The finale has you play as Superman carving through tag teaming bitches. Till you get to the godamned Batman where its rendered in a cutscene and Super wins. Setting up Injustice 2: Everyone has a Darksied.

This made me LOL for way too long haha.