When Batman and the rest of the Justice League stop The Royal Flush Gang from a robbery, they find out with the help of Cyborg that the Gang has been using a technology to walk through walls, and upon interrogation, realize that its not the Gang's technology. While Cyborg starts investigating behind the technology, Batman retreats to the Batcave.
Once Batman reaches there, he is forced by Alfred to rest. Once the cave is empty, Mirror Master (who had been hiding in the Batmobile) uses a LexCorp technology to hack into the Batcomputer and downloads crucial information on orders of an unknown boss.
Bane goes to the Slaughter Swamp outside Gotham City where he runs into Star Sapphire, Metallo, Ma'alefa'ak and Cheetah. The group then enter the Hall of Doom, where the are welcomed by Vandal Savage, who is also accompanied by Mirror Master. Already given $10 million each to attend the meeting, Vandal Savage offers them $100 million each for killing off each member of Justice League, to which, every one accepts. He then gives them fool-proof plans on how to defeat each member.
Bruce Wayne receives news from Alfred that the bodies of Thomas and Martha Wayne have been stolen. When Bruce confronts the employee who reported the incident, the employee reveals himself as Bane, and knocks-off Bruce into an empty grave. Bruce Wayne wakes up next to his father's grave, and forces his way out of the grave.
In his human form, Martian Manhunter celebrates his birthday with his friends when he receives a drink from an unknown woman. She later turns out to be Ma'alefa'ak, who had poisoned the drink, which would force Martian Manhunter to reveal his true form in front of everyone as well as be flammable. Ma'alefa'ak burns Martian Manhunter, and leaves him burning.
Cheetah poisons Wonder Woman with a serum which would show any person near the latter as the former. Intending on never giving up a fight, Wonder Woman also causes damage to Cyborg who eventually cures her.
Barry Allen finds out about a train robbery in progress by Mirror Master. He confronts him in his Flash atire, but is tricked into having a bomb attached to his wrist, which would go off if he tries to remove it, do nothing for 50 seconds or decelerate. This leaves Flash with no choice but to keep running at his fastest speed.
Green Lantern is called upon by the FBI, and is asked to capture a group terrorists, who are hiding in a salt cave, and have kidnapped 6 hostages. After defeating them all and saving the hostages, Green Lantern confronts the boss, who kills Carol Ferris (who later turns out to be someone that looked like the real Carol) before Lantern could do anything. Grieving over how he had caused Carol only pain, Hal resigns his Green Lantern persona. It turns out this was all a plot by Star Sapphire to cause Hal to doubt himself and cast fear in his heart. The whole plan was formulated by fooling Green Lantern with fear toxin, derived from Scarecrow's formula. It also turns out that the terrorists and the Carol look-a-like were all androids in order to fool Green Lantern.
Clark Kent receives a call from Lois Lane, who informs him that Henry Ackerson, a former Daily Planet employee who was laid off, was about to commit suicide. When Clark, in his Superman attire, approaches Henry, the latter reveals himself as Metallo, and shoots the former with a Kryptonion bullet, leaving Superman fatally wounded.
Assuming all members of the Justice League are defeated, Savage reveals his plans to kill off half of the human population with the help of a solar flare, and start over the world. As an offer to join him, Savage offers each of the members of the Legion of Doom a territory of the world, which they all accept.
Once Batman is back, he finds out that all of the members of the Justice League are under attack by the plans he himself had created, and one by one saves them all, and tells them about what had happened. The Justice League confronts the Legion of Doom, overpowering everyone including Savage, but are not able to prevent the solar flare. Cyborg deduces that the Hall of Doom would survive the Flare, and the Justice League works on preventing the Earth from any damage through it.
In a meeting, Superman announces that Vandal Savage has been imprisoned for life without parole. He also announces the inclusion of Cyborg as a member of the Justice League. He then announces a vote on Batman leaving or staying in the Justice League. Allowed to speak in his defense, Batman shows no regret over his motives and decides to leave the Justice League himself. Realizing that Batman is right, Superman gives Batman a Kryptonite bullet which the latter could use if Superman goes rogue as Batman leaves.