During Brainiac’s invasion of Krypton, Kara Zor-El and baby Kal-El are evacuated, but Kara’s bus is blown off course. A few years before the events of the first game, Batman and Robin fight a Regime attack at Arkham Asylum. Robin changes his mind and attacks Batman: he is defeated, but joins the Regime and kills Victor Zsasz.
Two years after Superman’s arrest and the fall of the Regime, Batman and the Insurgency are rebuilding society . Under the orders of a mysterious benefactor, Gorilla Grodd forms a group of villains: Scarecrow, Bane, Poison Ivy, Cheetah, Captain Cold, Reverse-Flash, Deadshot (after forcibly placing a nanochip in his head) and Catwoman (who apparently betrayed Batman) to form the Society. Batman dispatches Black Canary, Green Arrow, and a reformed Harley Quinn to Slaughter Swamp, where they defeat Poison Ivy and Scarecrow (although Harley is briefly dosed with Fear Toxin and forced to face the deceased Joker in a hallucination) before following the villains to Gorilla. City. After defeating Catwoman and Bane, they encounter Doctor Doom, who warns them of an imminent threat. After defeating Grodd, Canary and Arrow are kidnapped by Brainiac, the true master behind Grodd and the Society. He wants to collect Superman and destroy Earth. Brainiac takes over Batman’s communications center, Brother Eye, so he begins recruiting heroes to fight him.
He sends the Flash to help against the invasion of New Metropolis. After defeating Captain Cold, Deadshot, and Reverse-Flash, he meets Green Lantern and briefly fights him before realizing he can be trusted. Meanwhile, Catwoman, actually a double agent for Batman, saves Harley. Batman sends Lantern to recruit Aquaman for his course, and he agrees after Brainiac attacks Atlantis. While fighting off the attack, he encounters his arch-nemesis Atrocitus and thwarts his attempt to turn him into the Red Lanterns. Black Adam, Wonder Woman, and Kara (who was rescued from hyperspace by Adam and given the Supergirl mantle) attack Red Sun Prison in an attempt to free Superman and his imprisoned Regime members and defeat Brainiac. After defeating Blue Beetle and Firestorm, they form an alliance with Batman and the Insurgency on the condition of no killing.
Cyborg, Harley and Catwoman go to the Batcave to recapture Brother Eye. After defeating Poison Ivy, Bane, and Deadshot, Brainiac frees Grid from Cyborg’s body. After defeating him, they nullify Brainiac and free Brother Eye. Wonder Woman and Supergirl fight the invasion in New Metropolis and defeat Captain Cold, Reverse-Flash and Scarecrow. After defeating Cheetah, Wonder Woman prepares to kill her, but Harley Quinn intervenes, so Wonder Woman mortally wounds her. Horrified, Supergirl defeats Wonder Woman, heals Harley, and goes to the Fortress of Solitude to confront the actions of Superman and Wonder Woman. After learning of her evil, she defeats Nightwing, Black Adam and Superman. They then stop arguing when they realize that Brainiac has collected New Metropolis. Angry, Superman attempts to infiltrate Brainiac’s ship, but the shields apparently disintegrate him. The heroes refuse to hand Supergirl over to Brainiac, and Aquaman and Black Adam head to Kahndaq to release energy into the shields. Grodd brainwashes Canary and Arrow and sends them after the heroes. Upon defeating the heroes, they team up with Blue Beetle and face Grodd, but he reveals that he brainwashed Blue Beetle as well. They defeat Beetle and Grodd, and Aquaman kills Grodd to avenge Atlantis. They use the Trident of Atlantis to channel enough energy to destroy Brainiac’s shields.
