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Several years ago, the planet of Krypton was dying. As the malevolent alien lifeform known as Brainiac destroys its great cities, a young girl by the name of Kara Zor-El learns from her mother that the planet's core was destabilized. With their world on the verge of destruction, Kara learns that she is to take part in a plan to ensure Krypton's legacy lives on: she, along with her infant cousin Kal-El, would flee from Krypton for a new home, with Kara teaching him the ways of their people as he grows. As Brainiac's drone soldiers close in on them, Kara's mother places her in a shuttle and sends her into the stars alongside Kal's vessel.
Krypton explodes as the shuttles fly into space. Unfortunately, debris from Krypton's destruction crashes into Kara's shuttle, causing her to veer off course and become separated from Kal...
Several years ago, Batman was flying in his Batwing to Arkham Asylum, where Superman planned to execute the inmates detained therein. Damian, his son and protege as Robin, was accompanying him, even though Damian thought the inmates at Arkham deserved to die. The Batwing is suddenly redirected back towards the Batcave, forcing Batman and Robin to eject. They are intercepted by Cyborg, who allied with Superman due to his fellow Teen Titan Starfire and Beast Boy dying in Metropolis.
Batman manages to subdue Cyborg and, with Robin, proceeds to Arkham. As Robin second-guesses Batman's methods, they are confronted by Wonder Woman, who claims that the events of Metropolis changed the world, and the Justice League had to change with it. Batman subdues Wonder Woman, then uses her Lasso of Truth to extract Superman's location in the asylum.
Superman has the inmates of Arkham moved to a cell block within the asylum when Batman confronts him. Superman states that the inmates were irredeemable, and that his previous battle for "truth and justice" was futile. When Superman refuses to back down, Batman uses a red solar grenade to force him to fight on even footing and subdue him.
Before Batman can restrain Superman with kryptonite rope, Robin appears, holding Arkham inmate Victor Zsasz with a bladed Batarang to his throat. Batman warns him to stop, but Robin slits Zsasz's throat, calling Batman out on fighting his friends instead of combating the "real problem" and betraying him for Superman.
Batman is forced to fight his own son. Damian calls Bruce out on allowing the Joker to run free, putting blame for the deaths in Metropolis, of Lois, and of Jason Todd on him. Superman, deciding to make a tactical retreat, leaves Arkham with Damian.
The R&R has to wait, however, as Bruce is visited by Oliver and Dinah Queen: Green Arrow and Black Canary. He takes the two to his new Batcave to show them Brother Eye. They are joined by the reformed (but still quite unbalanced) Harley Quinn. Bruce and Harley explain that the world's infrastructure is left weak and vulnerable in the wake of the Regime's collapse, and the notorious Gorilla Grodd had established a new terrorist group known as the "Society", based out of Gorilla City. Grodd is up to something, and he is expecting a shipment of Scarecrow's fear toxin. To that end, Batman wants Oliver, Dinah, and Harley to stop the shipment.
In Slaughter Slum, Harley and her compatriots watch as Deadshot oversees the shipment in preparation for an attack the following day. Before they can act, they are captured by Poison Ivy. Harley is relieved at first to see "Red", but the relief is short-lived when Scarecrow confirms her allegiance lies with Grodd: Ivy sees Batman as no better for the enviornment than Superman's Regime.
Harley frees herself, Oliver, and Dinah, then subdues Ivy. When she goes to help Oliver and Dinah, however, she is hit by Scarecrow's fear toxin. Harley fends off Scarecrow, but is hit with an additional dose of his toxin which makes her hallucinate the Joker appearing before her. The Joker calls Harley out on her seemingly pretending to be a real hero and suppressing her "true" self as a madwoman. The Batman appears before her as well, and she prepares to stab him as he sit tied to a chair, but reconsiders at the last moment and fights back against her old "Puddin'".
The effects of the fear toxin subside and Harley returns to reality. Oliver takes out the boats shipping the toxin, but the commotion attracts the attention of the Swamp Thing. Harley fends of the Swamp Thing and explains the situation. Unfortunately, Scarecrow manages to escape.
Harley offers the Swamp Thing a place by their side fighting against evil. While the Swamp Thing declines the offer, he promises to aid them if their interests become mutual once more.
Meanwhile, Bruce sends Harley, Oliver, and Dinah to Gorilla City to extradite Grodd in the hopes of halting the Society. Within Gorilla City, the three witness as Grodd gives a speech to the gorilla army he had amassed. He is joined by his accomplices: Scarecrow, Captain Cold, Cheetah, Poison Ivy, Bane, Deadshot, and Catwoman.
Harley returns to the jet to wait for Oliver and Dinah while they make their move. After fighting they way past Catwoman and Bane, they are confronted by Doctor Fate: having saved them from Superman's wrath in the Regime's infancy, Doctor Fate warns them that a grim fate is awaiting Earth, and instructs them to escape with him to safety. When they insist on staying and helping Batman, Doctor Fate attacks them, but he is subdued. They wrist the Helm of Fate off of its wearer, Kent Wilson, who apologizes for having attacked them, being compelled by the Lords of Order.
After Kent makes his retreat, they chase down Grodd, subdue him, and place him in cuffs. Before they can leave with Grodd, however, the Society's "silent partner" makes his move: Brainiac's mothership appears over Gorilla City and abducts Oliver and Dinah. Onboard, Brainiac restrains the two and explains he came to Earth to seek out Superman, the one missing element of his collection of Krypton, which he destroyed after taking what he wanted of it to make his knowledge of the planet all the more valuable. Now, he has his sights set on Earth...
All the while, Kara is horrified to learn of Brainiac's arrival, and warns Wonder Woman and Black Adam that they need to hurry and rescue Kal.
Meanwhile, Barry Allen, the Flash, is stationed at a remote climate research center: he is struggling to fit in with his colleagues, due to his reputation as a member of Superman's Regime. When he learns of a crisis hitting Metropolis, however, he dons his red jumpsuit and hurries to the scene.
As he fights of Brainiac's drones, he is ambushed by Captain Cold and Deadshot. After fending them off, he is attacked once more by the Reverse-Flash, Eobard Thawne. Their fight leads them to Gotham, where Eobard reveals that he is unable to return to the future as a result of Superman's Regime killing one of his ancestors.
After the Flash drives off his doppleganger, he is approached by the Green Lantern, Hal Jordan. The Flash is suspicious of Hal, who was part of the Sinestro Corps during Superman's Regime. Hal, however, insists that he is prepared to fight in Earth's defense once more, having earned his Green Lantern Ring once more. After seeing Hal's resolve, the Flash decides to accept his aid.
When the Green Lantern arrives in Atlantis, Aquaman rebuffs his request for aid and tries to drive him off, resentful of the Regime's attempted conquest of his kingdom. After the two fight, they are ambushed by Cheetah, Bane, and Brainiac's drones. As Aquaman fights off the drones, the Green Lantern drives off the two Society interlopers.
All throughout, Hal struggles with an inexplicable, supernatural rage threatening to overwhelm him. This is the result of interference from Atrocitus, a Red Lantern. Atrocitus, accompanied by Dex-Starr, approaches Hal: even though he blames Hal for the death of his people while he was a Yellow Lantern, he sees the rage Hal felt as an opportunity to turn him into a fellow Red Lantern. Hal's willpower, however, proves more powerful than his rage, and he manages to drive off Atrocitus.
With Atlantis secured, Aquaman informs Hal that, unfortunately, he has to put the safety of Atlantis first.
The Flash circles the globe and pinpoints the positions of Brainiac's ships. Unfortunately, they don't have the means to mount an effective counterattack: Batman's most powerful comrades are busy protecting Stryker's Island, in case Brainiac tries to take Superman.
At Stryker's Island, Jaime Reyes, the Blue Beetle, looks after Superman's cell along with Jason Rusch and Dr. Martin Stein, the two entities that form Firestorm. Stryker's Island comes under siege, not by Brainiac, but by Superman's collaborators.
Black Adam moves to sabotage the generator powering the prison. Blue Beetle and Firestorm manage to fend him off, as well as Damian Wayne, now taking the name "Nightwing".
All the while, Wonder Woman and the escaped Cyborg prepare to free Superman. Kara finally reunites with her beloved cousin after having been separated for years following Krypton's destruction. Their relief is short lived as Blue Beetle and Firestorm move to subdue Cyborg before he can free Superman.
Kara attacks the two. Firestorm summons two rocks of Kryptonite to weaken Kara, but Kara manages to power through the Kryptonite's radiation.
In a last ditch effort to prevent Superman from escaping, Firestorm prepares to create a massive explosion that would destroy Stryker's Island. Batman stops him, however: with Brainiac proving too formidable a foe, Batman is left with no choice but to free Superman from Stryker's Island. The two form an uneasy alliance to fight against Brainiac.
Due to the Batcave's defenses, the unlikely trio have to go in through a backdoor under Arkham Asylum. Before they can go in, they are ambushed by Posion Ivy. Ivy uses pheromones to control Harley and force her to attack Cyborg and Catwoman. They manage to beat her, but the pheromones send her into shock. While one tries to stabilize Harley, the other fights and defeats Poison Ivy.
The three venture into the Underground and find the Batcave entrance, leaving Harley to defend the door. But upon entering the Batcave, the two are ambushed by Bane and Deadshot. Together, the two defeat the last of the Society members that had been waiting for them.
When they move on to the Brother Eye terminal, Braniac intercepts them and uses a virus to create Cyborg's fully-robotic duplicate: Grid. Grid tries to keep them from activating back-up power, but is swiftly defeated. The two bring back Brother Eye, and Batman reopens the old Justice League comm system.
Diana is knocked into the Ace o' Clubs bar, where she is ambushed by Thawne and Cold. By reflecting a blast from the Cold Gun, she incapacitates Thawne, but Cold is relentless: He wants revenge for her personal execution of Golden Glider, and doesn't care in the slightest if Braniac destroys everything around him as long as he gets it.
Superman appears before Diana after she drives off the two Society goons. At first, Superman appears to flirt with her, but suddenly attacks her. Diana quickly realizes she is suffering from a fear toxin-induced hallucination and fights back against Scarecrow, slashing him in the hand to prevent him from using his gas again.
Diana rushes back out and finds Kara at Cheetah's mercy, the Kryptonian girl weak to Cheetah's magic. Diana subdues Cheetah, and prepares to execute her. Harley objects, however: when Batman was discussing their plan for fighting back against Brainiac, he adamantly reminded everyone not to kill. A furious Diana attacks Harley, running her through with her sword.
Kara had long wondered why the symbol adorning her bodice, the House of El's coat of arms, inspired fear in the Earthlings rather than hope. Superman's actions following the death of Lois, and his stance on Harley and other "enemies", enlightens her as to why in the worst way imaginable. Likening Kal to the infamous Kryptonian war criminal General Zod, Kara prepares to leave, but is confronted by Nightwing and Black Adam, then Superman, who tells Kara the simple fact of the matter as he sees it: "You're either with me, or against me."
As Kent Wilson laments his inability to help the people of Earth, due to the Lords of Order siding with Brainiac; Brainiac's mothership looms over Metropolis, Batman, Superman, and Supergirl launch an offensive: attacking and defeating Brainiac, himself, would stop his beta ships in their tracts and spare Earth. Unfortunately, their every attempt to infiltrate the mothership is thwarted by a powerful barrier. Ultimately, Superman is powerless to stop Brainiac from "collecting" Metropolis. In a blind rage, he charges at the mothership once more, but is rebuffed. Kara is forced to watch in horror as Superman is hit with lasers from the mothership, with her beloved cousin disappearing in a powerful explosion.
With one hour to destruction, Black Adam hatches a plan to disable Brainiac's shields so they could infiltrate the ship: he could channel power from the Rock of Eternity in Kahndaq to attack the mothership, using Aquaman's trident to channel its immense power. They would need to work quickly, however: the magic spell that concealed Kahndaq would not be able to conceal the massive surge of power they would need.
As Black Adam opens the gateway that leads to the Rock of Eternity, Brainiac takes notice of the immense power he gives off. He orders Grodd to take his compatriots to Kahndaq and get a sample of the Rock. Grodd laments that his Society has disbanded: once it became clear what Brainiac intended to do with Earth, they dropped their flags and left. Brainiac offers him a new team to lead, and promises to reward him for his success.
As Black Adam and Aquaman prepare to pass through the gateway, they are attacked by Brainiac's drones, led by the mind-controlled Green Arrow and Black Canary. After fending them off, they are joined by Blue Beetle. After they pass through the gateway, however, Blue Beetle attacks them: he has fallen under Grodd's mind control. After subduing Blue Beetle, the two attack Grodd. As Grodd taunts them, telling them they are powerless before Brainiac, Aquaman runs him through with his trident, ending the threat he presented once and for all.
Batman finds himself surrounded by drones, but is saved from certain doom by the surprising appearance of Superman, who survived the attack from Brainiac's laser assault and was actually abducted.
Deep inside the mothership, Batman and Superman find Firestorm and the Swamp Thing, both having fallen under the thrall of Brainiac. The two manage to subdue Brainiac's victims, then use the signal disruptor to free them from Brainiac's control.
Within the heart of the mothership, the two are confronted by Doctor Fate: having decided that Brainiac brought true order to the cosmos, the Lords of Order had allied with Brainiac. The two subdue Kent, with Superman taking the Helm of Order and crushing it in his hands, freeing Kent from the Lords of Order's control once and for all. His relief is short-lived, however, as he is run through by one of Brainiac's tentacles.
Brainiac appears before the two, fighting off Batman. Superman attacks Brainiac, and succeeds in knocking him out, giving Batman the chance he needs to hit Brainiac with his signal disruptor. Cut off from his ship, the beta ships and drones deactivate. Unfortunately, without anyone to control it, the mothership begins to plummet towards the Earth. In desperation, and against Batman's warnings, Superman plugs his head into the ship. It takes every ounce of willpower he has, but he manages to prevent the mothership from hitting the Earth, saving a city below and the dozens of cities contained in the ship's database, as well as freeing Kara, who was to be dissected to study the effects of a yellow sun's radiation on Kryptonian physiology.
As Superman struggles to set the ship on auto-pilot, Brainiac lashes out at Batman. Batman fights Brainiac to prevent him from stopping Superman, and succeeds in knocking him out once more.
With Brainiac incapacitated, Superman succeeds in setting the ship on auto-pilot and, as they are joined by their allies, begins to restore the Earth cities that Brainiac had collected. Unfortunately, Superman could not save all of the cities before he is forced to stop due to overtaxing his mind: some remain trapped in the collection, but others have been deleted. Metropolis and Coast City are among the cities that Superman couldn't restore.
After regaining his stamina, Superman marches towards Brainiac. Batman stops him, however: he warns Superman that they need to keep Brainiac alive if they hope to restore all of the cities. Superman insists that he can do it himself, given time, and chastises Batman for not having the conviction to kill those who need to die for the sake of peace.
As the Justice League falls apart once more over differences of ideology, Batman slashes Superman with a dagger made from Gold Kryptonite, a substance that could leave Superman completely and permanently powerless...
Their battles eventually brings Clark Kent and Bruce Wayne together once more in the Batcave. The two admit that it was enjoyable fighting alongside each other once more, think back to the night they learned Lois was pregnant, and lament on how things have changed since her death.
"I miss the people we were then..." Bruce says quietly.
"Me too..." Clark agrees. But then, Superman kills the moment by sucker-punching Batman.
The two then come to blows for one final time, and when the dust settles, the victor is...
The righteous Dark Knight. Batman succeeds in subduing Superman. He takes the defeated despot to the Fortress of Solitude, where he uses light from Gold Kryptonite to render Superman powerless before sending him to the Phantom Zone, with Superman warning Batman that, in time, he would escape. How Supes plans to do this remains unknown, but Batman agrees that Superman can pose a a major threat even after being de-powered. After Superman is sealed away within the Phantom Zone, Kara laments how the symbol for the House of El has been warped to become a symbol of fear and tyranny. Batman reminds her, however, that what that symbol stood for depended on who wore it, offering a hand of friendship to Kara Zor-El and welcoming her into his circle of trust.
The corrupt Man of Steel. Superman completely overpowers Batman, who attempts to goad Superman into killing him and show him the villain he has become, but Clark simply cold-cocks him with a headbutt, not wanting the world to see Bruce as a martyr. With the last obstacle to his return to power dealt with, Superman kills Brainiac and uses the technology from the mothership to free Earth's captured cities, releases a veritable army of aliens willing to fight for him from Brainiac' collection that rivals the combined numbers of the various Lantern Corps, and re-establishes the Regime. He visits Kara in Stryker's Island, having placed her in the same red sun prison he once lived in and now wearing a suit resembling Brainiac's armor, and orders her to accept a place at his side. She refuses, but Superman warns her that if she doesn't, he'll forcibly make her one way or another. And to prove his point, he summons Batman, who, much to Kara's horror, has been brought under Superman's complete control using Brainiac's mind control technology...