1. Jim Gordon is again aware Barbara is Batgirl
2. Alan Moore Joker is the only Joker that survives

The Comedian, and not the Gangster? Interesting.

Bruce, Barbra and Jason discuss the multiple Jokers and the plan to create a 'better' one. Jason and Bruce briefly argue, Bruce is informed that Joe Chill has been abducted from Blackgate, he visits his cell and finds unfinished letters written to Bruce Wayne. He talks to a reverened about the letters, who tells him of Chill's learning disabilities. Bruce finds a letter addressed to Batman specifically, he opens it and finds tickets to the movie theatre that was showing Mark of Zorro the night of his parent's murder.

The three Bats arrive at the theatre and split up to look around. Babs and Jason are confronted by swarms of Jokers. Bruce confronts the Criminal Joker, who has Joe Chill hanging above a vast vat of chemicals. The Criminal wants Joe Chill to be the "Joker who matters' to Batman.

The whole time the confrontations are playing out, Chill's confession to the Comedian Joker plays out on the big screen. He knew who the Waynes were when he confronted them in the alleyway, it wasn't a random shooting. He picked his targets because he blamed them for the kind of lifestyle he was presently living and wanted payback. He felt bad after he realised he'd left their son without a parent. He apologises.

Bruce saves Chill and defeats the Criminal. Bruce then forgives Chill. Criminal tries to kill Bruce but is shot dead by the Comedian...the last Joker standing. He surrenders and he and Bruce have a chat in the back of the police van. Like in the regular continuity, Joker does know Bruce's identity but will never tell. He goes on to suggest that he created the Criminal Joker, but doesn't commit to that revelation, and also suggests the Criminal created him. It will remain forever ambiguous as to whether or not this was a long con by the Joker to try and break Batman and Gotham further.

Joker reveals the whole idea of trying to convert Chill to a Joker was his idea, and he takes great satisfaction in knowing that Bruce forgave Chill, he is now credited with healing Bruce's greatest wound, so that now he and he alone can be Batman's greatest pain.

Jason asks Babs if there is a chance they can be together, Babs doesn't think so. Jason departs, Commisioner Gordon asks Batgirl how she's feeling, and then suddenly says he doesn't want her involved with Red Hood. Babs says "that's my buisness..." and addresses him as "dad".

Jason isn't done trying to win Babs' heart though, and writes a love letter to her that he pins on her door, but the note falls off and is swept away by a cleaner.

Joe Chill is visited by Bruce in Blackgate, and he eventually dies.

Bruce tells Alfred that he figured out the Joker's identity a week after they first met, it's then revealed that the Joker's wife from Killing Joke is actually alive, having had her death faked and given a new identity by the Gotham police. She was in an abusive relationship and was heavily pregnant. Bruce tracks them down to Alaska where he watches over the family.