Alignments switch regularly in the main story, and for this reason the character selection screen is split into 3 tiers: Power (Right) Gadgets (Left) and DLC (Bottom)
Gadgets: Batman, Nightwing, Robin, Harley Quinn, Deathstroke, Joker, Black Spider, Lex Luthor, Catwoman, Green Arrow, Bane, KG Beast, Captain Boomerang, Killer Shark, Cyborg, Scarecrow, Black Canary, and Batwoman.
Power: Superman, Wonder Woman, Aquaman, Flash, Green Lantern, Starfire, Poison Ivy, Raven, Beast Boy, Superboy, Supergirl, Wonder Girl, Donna Troy, Sinestro, Arkillo, Saint Walker, Circe, Black Manta and Zoom.
DLC: Firstrorm, Doctor Fate, Blue Beetle, Deadman, Captain Atom, The Atom, and Amazo.
The game opens with the batmible, racing to a warehouse in the middle of nowhere, and you can see almost nothing but snow. The batmobile reaches the warehouse and batman quickly emerges, and rushes towards the warehouse. Screams can be heard coming inside as batman tries to open the door, but it wont nudge. Batman then looks at a window and realizes it is his opportunity inside. As he takes out his grapnel gun, the warehouse explodes and the camera zooms in on batman's face, witch is ridden with terror. We then see a large pause symbol appear and we then hear "This happened 5 years ago this day". The camera then zooms out to show that this was all a video and we then see a hologram of Lex Luthor, he is inside the nexus of reality. It is then shown that there is a council of Lex Luthor's from different dimensions. They hold a vote to see weather or not they should go and change reality, almost all Luthors agree that they should, thus they proceed. The camera zooms back into the screen and we see it rewind. This time batman makes it inside and grabs a dying robin (witch robin it is is unknown at this point) and calls the batmobile inside to drive him to the batcave, where alfred can heal him. As batman investigates he notices a bomb. He was about to run but he notices the bomb stops at 0:01. We then see Joker has been watching and stopped. He may have wanted Robin dead but never the big bat himself. He simply gases the room and batman tries to escape, but he gets snowed in and passes out. Joker emerges and finds a tiny box. He picks it up and notices a note on it. He reads it and exclaims "Oooh! Thanks lexy!" And drags Batman as the screen fades. We then are put in batman's eyes as he awekens. He looks around and is shocked that all his equipment is gone. Joker then comes behind him and puts a bag on his head. This makes batman forget all his fighting skills and joker lets him free, and easily defeats him. Joker then does many experiments on Batman, slowly driving him crazy.
One day Joker lets Batman free. He puts the bag back on his head, effectively giving him his fighting skills back. Batman gets up and turns towards the joker and says "BANG!" as he grabs Joker's gun and shoots him in the abdomen. He knows the Joker will get better and that's what he wanted. He planned to make the Joker's death slow and painful. But he had to wait. Batman returns to the batcave to find Alfred, very releived to see him, because he thought Bruce was dead. Batman simply laughs and throws a batarang at alfred, causing him to flee in terror, causing batman to laugh very hard. He then spins around in his chair in front of the Batcomputer. And opens up files. The pictures for Superman, Wonder Woman, The Flash, Aquaman, and Green Lantern. He then exclaims "Hmmmm...let's not show favoritism" and smirks. Then the pictures of Lex Luthor, Circe, Professor Zoom, Black Manta, and Sinestro appear. He then hears robin behind him. Robin is shocked because he knows what batman is doing. Bruce turns around in his chair, flashes a smile at robin, and says "Don't be scared, Daddy's home" and then laughs at the top of his lungs. Robin, being smart enough to know that he can't beat Batman one on one, flees to warn the Justice League of the shocking news. (More To Come)