Issue #1

Three years have passed following the deaths of Lex Luthor and Dick Grayson/the "Joker". Bruce Wayne has not been seen since. In the Batcave, someone unseen shatters a display case and removes the Batsuit from therein.

On the streets, a suspect is chased by Gotham City police officers but saved when Batman appears to attack their pursuit vehicles.

In a jungle setting, Wonder Woman battles a four-legged minotaur while her infant super-son, Johnathan, rides in a papoose on her back. Upon returning to the Amazons' new city, she learns that her truant daughter Lara is visiting Superman, father to her and consort to Diana.

Superman is now mysteriously iced over, seated on a throne in his rebuilt Fortress of Solitude. Lara speaks to him absently about the Kryptonian relics on display, including the Bottle City of Kandor. Upon looking closely at it, she discovers a distress signal.

Back in Gotham, Commissioner Ellen Yindel ponders the derelict Bat-Signal. Her career is mired by the media frenzy surrounding the Batman sightings and a new mayoral spokesperson trying to put words in her mouth. She answers a call reporting Batman's imminent arrest.

The ensuing chase results in Batman surrounded and abandoning a motorcycle. After considerable resistance, the cops manage to beat Batman down with night sticks. Disregarding the surprise of a female Batman, Yindel joins the arrest, unmasks her, and demands the whereabouts of Bruce Wayne. Revealed, Carrie Kelley claims the original Batman is now dead.^[10]

Issue #2

The beaten and bloodied Carrie Kelley is manhandled into a police vehicle. When prompted, she madly repeats her claim that "Bruce Wayne is dead" three times. She is incarcerated as a Jane Doe and Commissioner Yindel spends a month interrogating her, with mixed success. Carrie claims the aging Bruce Wayne finally succumbed to battle injuries after years of holding on. But when asked about his final resting place, Carrie only makes a sick joke and chides Yindel about her anti-Batman beliefs.

Back at his laboratory, Ray Palmer fills in Lara about the horrible consequences of his earlier attempts to resize Kandor. Baal joins the conversation through a wall-mounted speaker. Lara super-hears a summons from her mother and flies away in the blink of an eye. Baal and Ray continue talking, leaving off with Baal frowning when Ray makes a reference to God.

Following some media commentary, Yindel takes reports on the lack of protesters or resistance to Carrie's legal situation, implying that the Mayor is manipulating opinions. Yindel remotely oversees Carrie's prison transport. At a strategic point en route, Carrie whistles to trigger a non-lethal missile strike on the transport. The Batmobile (still refit to tank form per The Dark Knight Returns) advances on the transport. A waiting force of squad cars and drones scrambles to surround the Batmobile. As it continues to shoot police vehicles, Yindel orders a drawbridge raised to cut off its escape route. Police corner the Batmobile against the drawbridge, but find no one inside. Its afterburner fires, propelling it over the drawbridge. Carrie, who has wedged herself in the undercarriage, escapes when the Batmobile lands on the other side of the river.

In a desert, Ray attempts his Kandor restoration project involving cables connected to the bottle and a chest-mounted beam projector. After a blinding flash, the area is populated by full-sized Kandor citizens. However, Ray is shocked to see that some of their number are freshly dead and many more wear the raiments of a cult soon revealed to be twisted, fanatical, and polygamous. The regrown Baal introduces their leader as Quar. Quar redirects the beam on Palmer. Palmer shrinks to a tiny height and Baal steps on him. Quar orates about their new home and power. He picks up the bottle city, whose inhabitants no longer include any of his followers, and obliterates it with heat vision.

In the Batcave, Carrie disembarks from the Batmobile and approaches the Batcomputer terminal. Bruce Wayne stands there with a crutch and turns to look at her with an unreadable expression.

Issue #3

Now released from Kandor, the Kryptonians led by Quar make an announcement to the world, asking that they be acknowledged as gods or face destruction. Faced with this ultimatum, but recognising that he is too weak to face such a threat himself, Bruce takes Carrie to the Fortress of Solitude to inspire Superman back into action, who since The Dark Knight Strikes Again has left himself to freeze in the Fortress. When they reach the Fortress, Bruce strikes Clark with a sledgehammer to rouse him. Clark awakens to Carrie saying that Kryptonians are involved. While Superman agrees to help, Quar and his followers breach the Pentagon, demanding an answer to their ultimatum. The monitors around the room go black and Bruce (in his Batsuit) declares: "Go to Hell". At that moment, Superman arrives, but is shocked to see his daughter Lara now aiding Quar, declaring him a traitor to his own race.

Issue #4

Superman stands his ground, but refuses to fight back as Lara pummels him all across the world to the Fortress of Solitude. Quar cocoons Superman in black matter and orders his legion of Kryptonians to sink the Fortress into the ocean, and Superman with it. He then gives out an order to Gotham City demanding that they hand over the Batman or they will take it out on Gotham. As the city falls into chaos, Bruce orders Carrie on a special mission, giving her some sort of pill and her new Batgirl costume. Wonder Woman, meanwhile, stands alone on Themyscira in the rain, ignoring the call to action from Bruce. As Ellen Yindel waxes on the worth of the people of Gotham and that of the GCPD, Bruce in his Batman garb appears behind her and tells her to stop trying to drown out the needs of her people.

Meanwhile, Ray Palmer, revealed to still be alive, is sinking into a subatomic universe when he suddenly grabs hold of an atom, realizing that he might be able to fix his mistake.

Issue #5

With Gotham City under attack, Batman's followers bring Flash to the Batcave, but Batman is worried he cannot fix the Flash's broken legs. Meanwhile, Carrie Kelly, Aquaman and his army have found Superman in the Arctic. Aquaman gives Carrie Kelly a golden needle, saying it is the only thing that will free Superman from the matter he is trapped in, which she does. Back in Gotham, Batman prepares to fight Quar and his legions. Superman brings Carrie back to the Batcave, where the Flash is now attached to a computer to interfere with the weather. Using power from the Bat-Signal, the Flash makes it rain synthetic kryptonite, weakening the Kryptonians and causing them to fall from the sky by the hundreds. Batman, Superman (clad in a kryptonite-resistant suit of armor), and the people of Gotham bring the fight to them.

Issue #6

Thanks to the synthetic kryptonite, Batman, Superman, the GCPD and the citizens of Gotham are able to hold off the Kryptonians. The weakened Quar is held off by the Sons of Batman, who hit him with a barrage of bullets and an RPG. Lara and Baal return from their outing around the world after the kryptonite rain has fallen and are surprised to see the situation with the downed Kryptonians. Baal begins to kill the citizens and burns a squadron of Batboys to death with his heat vision. Carrie attacks Baal with the Batmobile, which he destroys. Baal grabs Carrie by the cape and hurls her through the air. Miraculously, she is able to land unharmed. When she is cornered by Baal, Carrie uses her slingshot and shoots him with a kryptonite pebble directly in the eye. Baal retreats, screaming in pain. As the Kryptonians retreat, Superman suggests pursuing them to destroy them once and for all, but Batman persuades him to let them go and so they can "lick their wounds". Quar uses his heat vision and hits Batman in the back, burning a hole through his chest. After he collapses, Superman removes Batman's helmet. Bruce makes Clark promise not to take him to a hospital and seemingly dies.

Issue #7

The story continues with the GCPD led by Commissioner Ellen Yindel and Carrie Kelly cleaning up the city. Yindel asks Carrie if what they fought for was worth it, since a lot of people died during the battle. Carrie responds by telling Yindel to fix the Bat-Signal so they can keep in touch. Meanwhile, the Kryptonians were able to regain their strength and Quar persuaded Lara Kent to capture her brother, Jonathan Kent, as their hostage. At Themyscira, Wonder Woman was able to sense the planned siege when she confronted Lara, who was attempting to kidnap Jonathan Kent. The Kryptonians realized that the Amazonians were just waiting for them, ready to attack. Meanwhile, the unknown location Superman went into is revealed to be the Lazarus Pit. Superman plunges Batman's body into the pit and Bruce Wayne comes out alive, physically younger, and in his prime once again. Bruce attacks Superman due to the effects of the pit, but Superman calms him down at the end.

Issue #8

At the Batcave, Carrie and the Flash deal with Batman's death, with Carrie hopeful that Bruce is still alive. Batman, now rejuvenated by the Lazarus Pit, appears with Superman. They receive a transmission from Wonder Woman in Themyscira seeking assistance, as the Kryptonians have declared war against the Amazons. Superman arrives to check on Diana, but the Flash warns Wonder Woman and Superman that Quar and the remaining Kryptonians, who ingested nuclear bombs, are all in one location and have started a countdown.

Issue #9

Batman and Carrie race to the Kryptonians, who continue the countdown. During this, Batman manages to swarm them with bats, causing them to inadvertently attack one another. Discouraged, most of the Kryptonians attempt to leave Earth, only to be killed by Quar. Batman and Carrie attempt to attack, but are stopped by Superman, who goes in their stead. After being berated and assaulted by the remaining Kryptonians, Superman surprises them by systematically taking them out, revealing to Batman that Superman had been holding back his true fighting ability all this time. Defeated, the Kryptonians attempt to go nuclear, revealing that they are planted on a fault line which will rip the planet apart. However, Dr. Ray Palmer manages to fix and reverse the effects of his shrinking ray, causing him to grow and most of the remaining Kryptonians to shrink, negating their explosives' effects to nothing more than mere firecrackers. Quar, going nuclear as well, attempts to run, but he is taken by Lara and sent to the Sun, where he detonates.

Two months later, Superman seemingly has disappeared. Batman comes to grips with his extended life. Carrie has altered her Batsuit to mimic Batman's and rechristens herself "Batwoman". Batman grows to accept her as an equal as opposed to a sidekick. It is also revealed that Lara survived the encounter with Quar.