In Gotham City, while running away from Batman, the Joker is surprised to be apprehended by... Batgirl, who he had crippled and left in a wheel chair several years earlier. When Batman and Robin catch up to them, the Joker escapes while they are distracted by seeing Batgirl.

Apparently in an alternate timeline, Batgirl explains to them that instead of crippling her, the Joker had killed her father, Commissioner Gordon. In this timeline, the Police, rather than working friendly with the Batman Family, view them as dangerous vigilantes and are ordered to shoot on sight. The new police commissioner is... Harvey Dent. Bruce Wayne and Barbara Gordon are apparently also involved in a romantic relationship.

Confused about reality, Batman retreats to the Batcave to search for answers. He consults Oracle, who exists simultaneously as Batgirl, paradoxically. He decides to visit Harvey Dent to try and talk some sense into him.

At Gotham City Police Headquarters, the Joker knocks out the entire Police Department and kidnaps Dent, bringing the corpse of Jim Gordon with him. When Batman bursts in to stop the Joker, after incapacitating him he finds that Harvey Dent has reverted to becoming Two-Face again. And the corpse of Commissioner Gordon is now just the regular and very confused Commissioner Gordon.

Batman leaves, and briefly visits Oracle to talk about the Crisis, and her other self, who continues to act as Batgirl even in their timeline. Batman determines he needs to find help, and he goes to meet with Superman on the outskirts of Metropolis.