In the aftermath of the apparent death of Batman, Gotham City becomes the site of a three-way war as Two-Face, The Penguin, and Black Mask struggle for dominance. With the Gotham City Police Department crumbling under the pressure, the Bat Family calls in help, all the while struggling to determine the answer to the big question: who will assume the mantle of the Bat?
The story begins months after Final Crisis with hundreds of criminals in Gotham attempting to rise due to the absence of Batman. Two-Face and the Penguin are leading a mob war while, unbeknownst to them, a third candidate arrives into the battle, Black Mask. After tricking Arkham Asylum's inmates into working for him, Black Mask begins his attacks on Two-Face and the Penguin, the strongest organized crime presences in Gotham.
Batman's various allies are trying desperately to bring order to Gotham. Nightwing leads the effort but refuses to become Batman despite Tim Drake's urging. Meanwhile, a man impersonating Batman begins his war on crime using lethal tactics and leaving slips of paper saying "I AM BATMAN." Drake begins a search to stop the impostor and dons an old Batsuit in order to demonstrate how the real Batman would have acted. While Damian Wayne irresponsibly drives the Batmobile, he is attacked by Killer Croc and Poison Ivy. Damian is saved by Nightwing, who ends up being cornered by Black Mask's men. The stand-off is interrupted by the Batman impostor, bursting onto the scene with dual firearms while proclaiming, "I am Batman!"
As the impostor takes down the thugs and escapes with Nightwing and Damian on his tail, Nightwing deduces that the impostor is Jason Todd.After a short quarrel, Damian is shot. At the same time, Two-Face and the Penguin are unaware of Black Mask's actions, and plan to attack one another. Tim finds Jason Todd's "Batcave" in a subway station, and is saved from a booby trap by Catwoman, who knows Tim is behind the mask. Jason ambushes them, disposing of Catwoman then getting into a fight with Tim before impaling him in the chest with a Batarang. Leaving him for dead, Jason exclaims, "One more to go."
Dick organizes a manhunt to find the criminal throwing Gotham into chaos, then leaves in search of Tim and Jason. He reflects that he has been lying to Tim and Alfred: He has no objections to becoming the new Batman, but was ordered not to in Bruce's prerecorded message for him, saying that Nightwing and Robin could carry the torch. While the GCPD contemplates the burning city, Damian has risen from the surgery table he is on and considers attacking Alfred to escape. While Alfred is quick to point out that he’s not in shape to fight, he does let the lad leave with his new chaperone, Squire.
Black Mask is seen sitting in the darkness, his mask in his lap, speaking to either himself or someone else, saying the "master plan" is about to begin.
Dick traces Tim’s signal to Jason’s “Batcave”, and discovers Tim's discarded cowl. Jason begins the battle proclaiming that he killed Tim and that Dick can join him as Robin. In an attempt to calm Jason down, Dick plays Bruce’s “last will” message to Jason. It implies that there is a deep, dark secret that Jason is hiding from his childhood (before becoming Robin). Bruce apologizes for not getting Jason the help he needs, saying that he still has a chance. Jason, however, becomes even more enraged at the message and continues his attack on Dick by detonating charges in his lair.
Tim, who barely survived Jason’s attack, is faced with a collapsing floor with the detonation of Jason’s “batcave”, and falls to his certain death, only to be saved by Damian.
While Dick and Jason move their fight onto a moving train, Jason reveals that he knows who the criminal mastermind behind Gotham’s downfall is, and Dick is left to wonder if the Black Mask is the same that was killed by Catwoman, or someone entirely new. As the fight escalates, Dick kicks Jason off the train onto the side of the track. Dick offers Jason his hand, but Jason merely says "I'll be seeing you sooner than you think", and plunges into the bay.
As Dick contemplates Jason’s mistakes, he walks into the Batcave, with Alfred and a new Robin present (Damian), to assume the mantle of the Bat.