After a flashback to the Waynes picking Bruce up at the police station after him being caught in the theatre, and deciding they'll see the movie together, that storm seen in all the "Zero Year" tie-ins has finally hit the main book, and while Gordon is helping evacuate citizens such as Harper Row and her brother, he gets a call from Batman, telling him to go to Wayne Tower, where the Riddler is ready to take control of the city once the power gets turned back on.
Batman's plan? Well since, Riddler stole a whole bunch of shit to have what essentially is a skeleton key hacking device, that is amplified to take control of the city, hovering above Gotham in a weather balloon, Batman's got to get up there somehow... CUE THE BAT BLIMP! Unfortunately for Bruce, once he gets to the balloon, Dr. Death is there, waiting for him.
Meanwhile, as the Batblimp nears Riddler's balloon, Gordon gets Dan Corrigan on the line, telling him that they can't turn on the power, but Corrigan doesn't like Gordon, and doesn't care, so that didn't work. Gordon's only shot now is to find the Riddler, and just like Batman said, he's waiting in Wayne Tower, specifically in Philip Kane's old office. Seems like Riddler was waiting for company though, and has got some string tied to his finger. I could explain everything in detail, but long story short, after talking about the strength of pullies for a bit, Riddler attempts to drop that 10,000 pound rock Kane had in his office onto Gordon. Though it didn't smash Gordon to paste, the rock did create a giant hole in the floor which Gordon falls into, allowing Riddler to escape.
On the balloon, Bruce and Dr. Death go at it, with each hit Death takes, making his bones that more grotesque. In the struggle, Bruce looses his signal jammer, so he has to resort to plan B, after getting Dr. Death's bones tangled on the railing. As Bruce is setting up some explosives, Death talks about the song "Tokyo Moon" and what it means, as it became a tradition to use in his family, his father and son both using it. We learn that Death's son was one of the men who died during Philip Kane's sponsored mission to find Bruce in the desert, which... okay. And Dr. Death continues on to say the "Tokyo Moon" song's true meaning is that love isn't enough to protect people and... Look, I don't know. Eventually, the console blows up, the trauma to Dr. Death is so much that his bones start going crazy and begin to grow into him, evidently killing him. If the situation wasn't bad enough, it gets worse, as Bruce finds that the explosion wasn't enough to take out Riddler's signal... and then the power in Gotham goes back on.
So sure enough, Riddler takes control of everything in Gotham. Explosions everywhere, the cables tying the blimps (which Loeb is in) to the buildings are detached, no pumps drain the water so the streets flood, Gotham is fucked. Gordon manages to get to some safety and gets back on the line with Bruce, who is pissed off and going crazy, saying he should have taken the call and this is all his fault. What is he talking about? Well, that call when he was in the dessert. If Alfred knew he was alive, that group of soldiers wouldn't have been sent looking for him, Dr. Death's son wouldn't have died, which I assume means he wouldn't have gone nuts, which means none of this would have happened. So naturally, given Bruce's issues with blaming himself for tragedy, the fall of Gotham is mirrored with his parent's deaths, which wouldn't have happened if he hadn't had snuck out to see the movie.