The Justice League, with assistance from Cyborg, stop the Royal Flush Gang as they attempt to rob a diamond vault using complex technology that allows them to pass through solid objects. Wonder Woman uses her lasso of truth on the leader to find out who gave them the technology. The leader, despite being under the influence of the lasso, says that he does not know who gave them the technology. Martian Manhunter uses his mental powers to scan the minds of each member of the gang, none of them know the origin of the device. Meanwhile, Vandal Savage plots to exterminate the greater part of the human population and start a new civilization, having discreetly given the technology to the Gang in order to test it. To ensure that the Justice League is unable to stop him, Savage hires Mirror Master, who hacks into the Batcomputer and steals contingency plans devised by Batman to incapacitate his League teammates should they ever go rogue. When Mirror Master asks if he wants him to find Batman’s true identity, Savage declines stating that he already knows the true identity of Batman. Savage assembles Mirror Master and a group of other supervillains (consisting of Bane, Cheetah, Ma’alefa’ak, Star Sapphire, and Metallo) with personal vendettas against the heroes and pays them to simultaneously attack the members of the League using the stolen plans, albeit altered to be lethal. When the supervillains agree with Savage’s plan, he welcomes them to the Legion of Doom.
The villains each do their part to take out each member of the Justice League:
Batman, as Bruce Wayne, is informed by Alfred Pennyworth that the bodies of Thomas and Martha Wayne have been exhumed and are missing. When Bruce arrives at his parents’ graves, he is ambushed by Bane. The emotional distraction is enough to grant Bane the upper hand and render his adversary unconscious. Bruce is then placed into his father’s coffin, which is reburied, hoping to kill him through asphyxiation. Bruce is left a phone with a message from Bane taunting him and with the skeletal corpse of his buried father, both of which angers and motivates him to break out of the coffin using keys to his house, which he holds between his knuckles, leading to his hand to bleed as he punches the coffins lid. He soon realizes that the League has been attacked using his own contingency plans, plans he constructed after having studied the others for physical and psychological weaknesses in the event that the Justice League either went to the other side or have succumbed to mind control. With help from Cyborg, he saves his teammates one by one.
Wonder Woman is attacked by Cheetah who scratches her arm sending nanomachines into her bloodstream. The nanomachines attach themselves to her brain stem and begin broadcasting directly into her visual and auditory sensors, causing Wonder Woman to believe everyone she sees is a duplicate of Cheetah. Since she would never surrender, she will force herself to fight on until her body gives out from the drugs the nanomachines were carried in, causing her to suffer an epileptic seizure or a heart attack. Cyborg adjusts his sonic emitter to a frequency that neutralizes the nanites.
Martian Manhunter (in his human identity of John Jones) is celebrating his birthday with his colleagues from the police force. He receives a soda from a mysterious woman (who is actually Ma’alefa’ak in disguise). The drink is laced with magnesium carbonate, which is disruptive to Martian biology and leaves the Manhunter struggling to maintain his form while sweating out the highly flammable magnesium. Ma’alefa’ak uses a lighter to set his enemy on fire (Martian Manhunter’s only weakness) leaving him to constantly burn for weeks or longer without the possibility to extinguish the flames, even when he goes into the nearby ocean. Batman provides Cyborg and Wonder Woman with aluminum oxide that when injected into the Martian by Wonder Woman, neutralizes the magnesium.
The Flash is lured into a trap by Mirror Master, who pretends to rob a train. The villain uses a hologram of an elderly woman to create the illusion that he had a hostage. He then tricks the Flash into placing his arm into a booby trap that attaches a bomb to his wrist. The bomb will explode and kill everyone within three miles if he tries to remove it or if he does nothing. The only way to prevent the explosion is to run and never decelerate, but even the Flash cannot run forever. Batman instructs him to run and vibrate his molecules through an entire iceberg in the Arctic to get rid of the bomb. Flash just barely manages to get away from the blast radius. Green Lantern is called upon by the FBI to deal with a group of terrorists who have taken hostages into a salt mine. However, both the terrorists and the hostages are sophisticated androids. During the rescue attempt, Green Lantern is fooled into thinking that innocent lives were lost due to his overconfidence, having been exposed to a synthesized version of the Scarecrow’s fear gas that undermines his will. Finally, Star Sapphire shows up and exploits his fears, convincing him that he does not deserve the power he wields. Green Lantern renounces his ring, without which he cannot escape from the collapsing salt mine, and resigns to his fate. Batman shows him that the female hostage in his arms was an android when he takes its head off and offers him an antidote to the gas. Jordan rejects it and reestablishes his willpower, which instantly removes the effect of the fear gas. He then summons his ring, and once again becomes Green Lantern.
Superman is lured to the roof of the Daily Planet by a disillusioned former employee named Henry Ackerdson, who aims to commit suicide. Superman tries to talk him out of it, and appears to have succeeded when Ackerdson, who is actually Metallo in disguise with fake skin that resembles Ackerdson, unexpectedly shoots the hero instead with a bullet made of Kryptonite. Superman’s physiology makes it impossible to extract the Kryptonite bullet through conventional means. The Kryptonite bullet is surgically extracted by Cyborg, who uses a Kryptonite scalpel laser, and Martian Manhunter, who shapeshifts his fingers and gets the bullet out, and Superman regains consciousness. The Justice League retreats to the Watchtower, where Batman reveals that he was the real mastermind behind the attacks with the use of his contingency plans against the League should they become a threat to the world. However, he also had a contingency plan in place should the Batcomputer ever be hacked: a tracing algorithm hidden in his files. This enables the League to track down the Legion of Doom. The villains are subdued, but the heroes fail to prevent Savage’s scheme to orchestrate an apocalyptic cataclysm with a powerful solar flare. Using information obtained by Cyborg, Batman devises a last-minute plan to use the Hall of Doom’s technology to phase the Earth so that the flare can go through it and the League barely manages to save the Earth.
In the aftermath of their victory, the Justice League adds Cyborg to their roster and mention that the World Court sentenced the immortal Savage to life imprisonment without possibility of parole. Superman calls for a vote on Batman’s continued membership in the team, following the revelation of Batman’s breach of trust. However, Batman defends his plans and expresses no regret over his actions, again criticizing the other members for not understanding the potential danger of a rogue Justice League before quitting the team without them even beginning to vote. As Batman prepares to leave the Watchtower, Superman questions him about the nature of his contingency plans. Batman explains that the original plans were only meant to immobilize the Justice League, that Savage altered them to be lethal, and that exhuming the bodies of Thomas and Martha Wayne and then burying Bruce was entirely Savage’s idea. When Superman asks Batman if he is still arrogant enough to not create a contingency plan to stop himself, Batman replies there is one: the Justice League. With his own trust in Batman assured, Superman hands him the Kryptonite bullet for Batman to use if necessary and teleports Batman out of the Watchtower. The Justice League then looks down at Earth saddened that Batman decided to leave.