Tokyo, 1946, probably Doctor Death watching lounge singer during the war, I don't know! Moving on! Batman is getting shot at, and the GCPD knows his every move and tactic. Clearly, Bruce was set up, and his usual tricks of smoke bombs, grappling away, or escape vehicles have all been anticipated by the GCPD, so he has to get creative, and uses a gas canister to propel himself through the water, and into the bay, where James Gordon waits for him...
Surprisingly, Jim is offering Batman a hand, telling him that the police will find him before he's able to swim to shore. Bruce reluctantly gets on Jim's boat, getting Jim to take off his glasses while he removes the damaged cowl... nice little nod to Year One.
Anyways, Bruce asks how the GCPD knew about his location and tactics, turns out the Riddler tipped them off, and it gave Loeb enough of an excuse to wage war. Gordon tries to tell Batman that he's attempting to balance the scales, but Bruce is skeptical why he should listen to Gordon. The reason Gordon gives? Bruce Wayne.
Gordon fills Batman (not knowing it's Bruce) in on the other side of the story we heard last issue. That night after Gordon found Bruce skipping school, and got a gift of that coat, Gordon decides to investigate what the pay off was for, and finds a dog fighting ring in the back of the laundry mat, along with his partner. Gordon threatens to go to Loeb, who is also on the payroll, then threatens to go to the press. It's at this point, Gordon is thrown into the pit with the dogs, and people start placing their bets, most cheering for the dogs. Gordon eventually makes it out alive, putting a gun to his partner's head. Corrigan tells Jim that he bet on him and he should think about it, while threatening his family.
After the dog ordeal, Gordon then walked his beat, to prove a point, and he managed to get all the way to Park Row to hear two gunshots, and see Bruce Wayne, who was so hopeful and trusting in Gotham that afternoon, broken, crying over the bodies of his parents. So now with Bruce Wayne having returned to Gotham, trying to make it better, it's given Gordon some hope, and maybe that's why he's starting to see the value in Batman. Bruce tells him to stop the boat, Gordon turns around to see him gone, asking about his glasses, but finding them in his pocket just in time not to crash into the dock.
Back in the bat cave, Bruce and Alfred are going over a sample from Doctor Death, finding it too contaminated, with multiple sources of DNA. Alfred gets on Bruce's case again, trying to get him to accept help from Gordon, but Bruce tells Alfred that his help is all he needs. Alfred doesn't buy it, claiming he doesn't think Bruce trusts him. Then we get into some Alfred dropping knowledge mode, dissecting the concept of Batman. Alfred doesn't believe Bruce is suspicious of himself because he'd always report on Bruce's behavior to his parents, or because Bruce thinks Gordon is crooked. What Alfred believes is that Bruce is angry with them, and is using Batman as a form of punishment. Bruce doesn't follow, so Alfred tells him that he's making them all bare witness, making them watch him do what no one else could do for him. Alfred warns Bruce that if he doesn't accept their help, he'll become a demon of vengeance, rather than the symbol of justice he'd hope to be.
Bruce doesn't respond to Alfred's warnings, having deduced where Dr. Death may be: The catacombs. Usually a tourist attraction, not anymore since the power went out, and it explains all the DNA samples Bruce found from the Doctor. Sure enough, Bruce finds Dr. Death's lab, but is surprised to learn he's not acting alone, and the killings were to cover up stolen tech. But for who? The Riddler of course, who after Batman failing to solve his first riddle, is ready to unleash a doomsday machine on Gotham, with his latest riddle, but intends to flood Batman out before it can be solved.