The Joker (for reasons unknown) decideds not to try to drive Gordon insane, and doesn't shoot Barbara. Nothing much changes, till Jason Todd finds his Dad's old stuff. He goes searching for his mother, and Batman, without the Joker to worry about(since he isn't searching for him, and doesn't find the nuclear bomb) goes after Jason.

Meanwhile, the Joker decideds to use the nuclear bomb on Gotham city. Since no one believes that he has a nuke, they don't pay his ransom, and Joker uses the nuke, wiping Gotham city off the map. Batman's caught up with Jason Todd (in a Egypt, perhaps), and both of the learn about Gotham city on the news. Batman snaps upon hearing the destruction of Gotham, and kill Jason, blaming him for the fact that Batman wasn't in Gotham to protect it.

Superman goes into Gotham to search for survivors, stopping by Wayne Manor (which being outside of Gotham, and the Batcave being underground, Batman might've survived) Unfortunatly, he finds Alfred's irradiated body. He learns that Jason Todd has been found dead, and he instantly realizes why. He stops his search for survivors, and goes looking for Batman.

He eventually finds Batman, who fights him(if you can call it a fight, Superman just lets Batman hit him) for a while, till Batman breaks down, falling to his knees, crying. He pushes something on his utilty belt, and he vaporizes, having ignighted a small bomb. Superman looks at the scar on left on the earth, and begins to weep himself.
(in the background would be Joker's corpse)

Fade out.