My theory on the sequel: the movie opens with the world fearing Superman and the destruction he and the Kryptonian invaders caused in Metropolis. Batman captures Superman, seeing him as far too dangerous to remain among the rest of the world, using advanced technology suits and of course, kryptonite, to subdue him and hold him in cell with ultra red lighting to take away his super powers.
Doomsday comes to Earth, either as a being sent from the outer reaches of space, or more likely, as a creation of Lex Luthor's as a response to Superman's existence. Batman tries to fight him and loses miserably. His only option is to release Superman and fight him together.
Not really sure where Wonder Woman would play into this.
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