After returning from the alternate Earth of the Injustice Syndicate, Batman finds himself wanted for crimes committed by his counterpart Owlman, who escaped the Batcave. Batman swings away from the police and helicopters go in pursuit. Reading a newspaper, Batman discovers that the phase oscillator displaced him three weeks in time.
Batman spots a figure fleeing from a bank: Owlman, disguised as Batman. Batman goes after his counterpart but the two are too evenly matched. Owlman is impressed that Batman has defeated the Injustice Syndicate, and Batman realizes he wants the phase oscillator so he can go back, free the Syndicate, and invade Earth. Owlman flees as Green Arrow arrives and pins Batman down. He’s understandably skeptical of Batman’s claim that there’s an imposter. Batman distracts Green Arrow with an exploding bag of money and escapes through a secret tunnel. Green Arrow calls in Aquaman, Blue Beetle, the Atom, and Red Tornado, and tells Plastic Man his assistance isn’t required.
Blue Beetle spots Batman and opens fire. Batman short circuits the scarab but Plastic Man wraps himself around Batman. Batman blinds him with a smoke capsule and escapes through another tunnel, only to find Red Tornado waiting for him. Batman manages to blind the android and escape down an alleyway, and discovers that Owlman has reprogrammed the Batmobile. The heroes trap Batman in the dead-end alley but suddenly a figure pulls him into the shadows and inside a nearby warehouse. A shadowy figure is waiting for him: the Joker, angry that Batman has tried to out-criminal him.
Joker draws a gun only to reveal it’s a gag weapon. Batman punches him and Joker explains that he wants to be the hero’s partner. He soon realized that the “new” Batman was an impostor. Batman is reluctant but Joker points out that Batman can’t beat his counterpart and vice versa without an extra edge like the Clown Prince of Chaos. Batman considers the offer but they’re interrupted when Plastic Man finds them. Joker reveals his hidden Jokermobile and it bursts out into the streets. The heroes stop it only to discover that Plastic Man is bagged up inside.
Batman summons a spare Batmobile and they drive away. Batman demands that Joker promise not to harm anyone and the Clown Prince agrees. He starts fiddling with the dashboard controls and knocks himself out with anesthetic gas. Batman wakes him up in the Batcave and the Joker admires Batman’s collection of trophies. Batman realizes that Owlman examined the files he keeps on ways to neutralize his fellow heroes. Sure enough, Owlman captures the heroes one at a time using Batman’s techniques. They prepare to leave and Joker gasses himself unconscious again. Batman wakes him up once they’re on the way back to Gotham City.
Batman tries to contact the heroes and reaches Plastic Man. He doesn’t believe Batman’s warning and is captured. Batman and Joker arrive and Batman fights his counterpart. Joker produces a bazooka and opens fire, only to immobilize Batman while Owlman escapes. He tires to run them down and Joker uses Batman’s grapple to lift them both out of the way. They go after Owlman, who contacts them by radio and offers to trade the heroes for the phase oscillator. Batman refuses and Owlman starts going after pedestrians. Joker takes the wheel while Batman rescues the civilians, only to discover they’re afraid of him. Owlman drops mines around a boy and Joker reluctantly comes to the child’s rescue. The boy praises his new hero, Clown Face.
As they continue the pursuit, Joker wonders why Batman is taking a chance on him. Batman remembers how the Red Hood, Joker’s counterpart, was a hero on the alternate Earth. He then notices a new Batsignal in the sky.
At a wax statue factory, Owlman has assembled a team of villains and has put the captured heroes in death traps. Batman and the Joker arrive but are quickly overwhelmed. Owlman offers Joker his own death trap to dispose of Batman in return for the Clown Prince joining his team. Joker considers the trap and then admits he’s just not a hero. The trap drops on Batman and fills with hot wax.
A wormhole appears behind the villains and Batman emerges, carrying the phase oscillator. The villains take the phase oscillator but Batman explains that he knew Joker would betray him. He used the wormhole to not only teleport to parallel dimensions but spent a week of time doing so. In his travels, Batman has assembled a squad of six alternate Batmans who emerge from the wormhole. The two sides battle and the Batmen battle the villains and free the captured heroes. Batman and Owlman fight and the Joker tries to help his new ally. He throws a bomb which explodes, blinding both villains. They fight over who will kill Batman, unaware that Batman has grabbed the remote for the wax deathtrap and imprisons both of them.
Later, the authorities take the villains away and the alternate Batmen take Owlman through the wormhole and back to justice on his home Earth. Batman talks to the Joker, who admits that they could have been friends. However, Joker warns his nemesis that the next time he’ll have the final laugh.