Ras Al Ghul steals Batman's secret files and uses them to incapacitate the JLA. This is in service of a larger plot for mass destruction of the human race, as he renders all forms of communication useless. The JLA survives the assault and rallies to thwart his plans, but are shaken by the breach of trust by Batman.
Bruce Wayne goes to visit his parents grave and finds it missing. He then goes out to find their bodies. Meanwhile, Ra's Al Ghul is at his lair, he is angry that one of his men had fed an endangered creature with chocolate and killed it. He reveals he has a giant zoo of animals that were thought to be extinct. He begins to talk about a plan that will destroy the JLA. J'onn J'onzz is flying over a forest when Talia Al Ghul and a group of men shoots at him. Struck by the missile, J'onn is perplexed that it had no explosive payload, but is quickly alarmed when he sees microscopic vision that there is a cloud of tiny nanobots swarming. Suddenly, he finds himself engulfed in flame, his greatest vulnerability.
A while later, Wonder Woman and Flash respond to a ferocious forest fire. They race each other to the site and a figure on fire seemingly attacks them. After using a whirlwind to deprive the fire of oxygen, they realize that it was J'onn. Meanwhile, at the UN building the Atlanteans and humans argue for peace when Aquaman and Plastic Man disrupt the meeting because they had received a tip about a terrorist attack. They find the terrorists and they fire a gas grenade at Aquaman while the other fires a flash freeze beam at Plastic man and he is completely frozen. One of the terrorists cracks Plastic Man's frozen figure with a hammer and smashed him to pieces. Aquaman is rendered terrified of water and denies water he needs to survive.
J'onn is taken to the Watchtower where he is placed in a tube filled with water to keep him from catching fire in contact with air. Plastic Man meanwhile is being defrosted and Superman calls Batman, who is hijacking a helicopter. Superman warns that the Justice League is being attacked but Batman says he's busy. Wonder Woman and Flash decide to go over to Kyle Rayner's (Green Lantern) apartment because he hasn't responded yet. Superman goes over to the Daily Planet. Ra's, meanwhile, activates his Tower of Babel and all written words become unreadable. No one is able to read anything. Superman was first to notice this and he tries to control whatever is happening. Wonder Woman and Flash are unaware of this as they go Kyle's apartment in civilian clothes. They arrive only to find that Kyle was now blind.
Aquaman is trying to figure out how they found J'onn and him and attacked them. Although he is barely conscious, he has that 'Eureka' moment and figures out that the attackers were using the Leagues own tracking devices. He tries to warn them but before they could the bad guys attack them. Aquaman contacts his base in Atlantis and asks them to bring something for him. Wonder Woman and Flash change into their costumes and fight the mysterious attackers. Wonder Woman is hit by a ray gun and she thinks that she sees someone as powerful as her attack her. Flash is hit by a velocity bullet and he is vibrating non stop.
Meanwhile, Batman invades Ra's lair he arrives and finds that his parent's bodies are hung over a Lazarus Pit. Ra's offers Batman a chance to resurrect his parents. Batman refuses and Ra's says he knew that it was the decision he would make. He then takes out a red kryptonite sample and Batman looks on horrified. Talia meanwhile arrives at Kyle's apartment, Kyle goes berserk and Talia helps in stopping him. Talia alludes to a mysterious designer of the traps, J'onn bursts into the room and is wearing an Atlantean suit filled with water. He tries to get things under control but Talia knew his powers were limited because of the suit, she hurls Wonder Woman's Tiara and cuts off a part of the suit. J'onn begins to catch fire again but Superman arrives after putting a force field over Metropolis. Talia still looks confident and she takes out a piece of red kryptonite, Superman begins to feel weak but suddenly his skin becomes transparent and absorbing sunlight suddenly becomes painful to him.
Batman, meanwhile is still at the Himalayas in Ra's base trying to get away. He manages to get out of the base as Ra's men chase him across the mountain. Batman shouts through the communicator that he was the one who designed the League's traps, the signals trackers and they were all his.
He says that Ra's has stolen his equipment to incapacitate them. Ra's meanwhile is calmly sitting in a room, as the scientists prepares to do something. Batman still running says there are ways to counter the traps but before he could tell them Ra's presses a button and Aquaman couldn't understand what he was saying.
Batman is cornered at a mountain peak, he jumps off the mountain and the henchmen assumes he is dead. Aquaman tries to teleport Superman and the others but he falls unconscious and an awakened Plastic Man teleports them back to the Watchtower. Talia returns to her father's base and she begins to question her father's motives. Ra's Al Ghul tries to reassure her, then one of the men arrive and says that Batman has perished in the mountain side. Talia slaps the man in anger and walks away. The man walks away and into the shadows and he is revealed to be Batman in disguise. Aquaman wakes up in a desert and finds himself very comfortable there, but he is actually in a water tank and the desert is only an illusion J'onn is projecting into his mind. J'onn uses his x-ray vision to guide Plastic Man's finger as he tries to remove the nanobot in Wonder Woman's brain,while Superman is trying to burn off his excess power. He had become so powerful that he can hear a grasshopper's heart beating in Brazil. J'onn figures out that Kyle's blindness is actually a post hypnotic suggestion and when he takes off his Power Ring he begins to see again. They were also able to get vibration bullet off Flash. Even on the moon Superman can hear the world panicking as fires and riots burn down cities. No one on earth can read or understand what anyone is saying.
Batman calls the League for help on a secure line shielded from Ra's Tower of Babel. He asks them to follow his signal to a certain place. Superman thinks its a trap and he goes there alone, he meets with Batman who says that he will explain things later, but they are going to need J'onn's telepathic powers to communicate through their minds.
The JLA along with Batman arrive at a snowy summit. J'onn and Aquaman are at the Watchtower. Batman says through the telepathic link J'onn provided for the Leaguers that he has found Ra's tower of Babel. Two fighter jets arrive and Wonder Woman and Green Lantern goes after them. Kyle wants this to finish this up fast since they'll find out why Batman exploited them. The JLA members manage to hold off the defenses as Superman and Flash infiltrate the Tower. A red alarm sounds and they couldn't understand their own thoughts. Superman relays his last thought to Flash telling him to get out. Superman burns off the excess energy in him by blowing up the tower with his heat vision. Superman begins to walk out of the rubble and he begins to fall unconscious. Batman says that it's only residual side effects of the red kryptonite and that Superman will recover.
Talia contacts them through a separate tower where she is transmitting her words to the JLA's minds. She says that the disruption of language was merely a distraction. With the world's defenses now weakened Ra's Al Ghul is going to set two attacks one in Turkey and the other somewhere else. They are going to launch a canister over Turkey where it will release a nuclear material where it's going to kill half the city's population. Talia says she's telling them this because she is tired of her father's constant plans of ruling the world and only to fail. Before she could go any further someone shoots her in the leg. The attacker says that she said too much and the JLA cannot stop. He then cuts off the transmission.
J'onn takes off his protective water suit, since Martian's can shed their skin, the nano bots are off of him. He then goes into the same tank as Aquaman in attempt to help him lose his fear of water. He makes him aware he is in a water tank and tells him not to be afraid and to change his fear into something else, with no choice, he tells him to turn his fear into anger towards Batman. At the snowy region, Batman says that they should split up and he and Superman will go towards Ra's headquarters while the rest goes after the canisters. Plastic Man is reluctant to trust Batman but he says that they will talk about that later. Flash super speeds towards the location of the first canister, Green Lantern, Wonder Woman and Plastic Man are behind. As they fly off towards Ra's headquarters, Superman asks Batman why he did it.
Wonder Woman, Green Lantern and Plastic man arrive to find that one of the terrorists have opened the canister near a city and Flash was standing near the man. He was vibrating in his place because if he moved he might spread the nuclear material. Green Lantern puts a protective force field over them and gas mask over to nearby people. Plastic man and Wonder Woman goes after the second one. Ubu brings in the attacker who shot Talia. Talia was missing but the man claims he shot her in the leg. He believed that Ra's would be proud of him. Ubu asks his master's permission to drop the man to be eaten by a rare species of lions. Ra's grants him permission to do so.
Batman and Superman arrive at the mountain side, Batman recalls to Superman the time when an alien named Agamemno gave some criminals access to JLA's bodies. Batman says that the traps were meant to be fail-safe for such an attack. They arrive just when the man was dropped to be eaten by the lions. Superman saves the man and Batman tries to go after Ra's, only one problem Batman has to go through two lions and a tiger. The remaining canister is in the hands of two terrorists, one of them tries create a distraction by shooting to the crowd. The other goes to the roof to open the canister and release the nuclear material into the air. The first terrorist shoot to the crowd and Wonder Woman stops the bullets from hitting the targets. Plastic Man captures him and Wonder Woman flies to the rooftop. The man tries to get away but Wonder Woman lassos him before he falls off the building. Unfortunately, he bumps into two kids and they fall off the building.
Superman uses the metal around him to trap the tiger and lions that were about to attack him and Batman. They go after Ra's and Batman tells Superman that Ra's still has a weaker form of the red kryptonite and that he should after the Wayne's coffin. Superman goes after the coffins but finds the red kryptonite on the coffins. Batman goes through Ra's men and he presses a button and the coffins begin to fall. Aquaman catches the weakened Superman with the grapnel hook of his arm, J'onn flies over and catches the Wayne's coffins before they fall to the Lazarus pit. Batman goes after Ra's but he has already escaped and promised that Talia will pay for her betrayal. Batman however was able to capture Dr. Kant the biologist who had designed the Tower of Babel. Plastic Man caught the kids before they had hit the ground, Wonder Woman negotiates with the terrorist. With the help of the Lasso of Truth she convinces the terrorist to give up.
The League returns to the Watchtower. Batman is waiting in another room while the other members vote for whether Batman should be excluded or whether he should stay. Everyone votes and 3 for membership and 3 for expulsion which leaves Superman to take the last vote. Each member had their own reasons for excluding or forgiving Batman.
Voted For Expulsion
- Wonder Woman: She understands Batman's reason's for exploiting her weaknesses but she believes that he would be a weakness in the future.
- Aquaman: He thinks that they had earned the world's trust but his decision was affected due to his anger towards Batman.
- Plastic Man: He was still traumatized by the fact that he was frozen and smashed to pieces. Batman himself stated that he was afraid of how Plastic Man's mind might react when he was designing the countermeasures.
- Superman: At first no one knew how Superman voted but in JLA #50 it is said he voted for expulsion.
Voted For Membership
- J'onn J'onzz: He himself had kept information and dossiers of the League and has since been forgiven by the League. J'onn saw expulsion unnecessary because he somewhat understands why he did it.
- Green Lantern: Kyle may still be new to the League. But he remembers the events of Coast City and Hal Jordan. He thinks that Coast City might still exist if Batman's traps existed then.
- Flash: Wally was only a kid during the Argammemo case and it was Barry Allen's days as the Flash. He remembers how people including himself were afraid and knows that those measures might have helped then.
After the vote is discussed, they head to the room where Batman was waiting but find him already gone.
JLA Secret Files
In JLA Secret Files, it is reveled that it was Talia who infiltrated the Watchtower. Even then she is beginning to doubt her father. Her father's organization had learned about the plans through tiny hints during Batman and Oracle's communication. Talia got into the Watchtower through the League's food and supply teleporter. She fools the Tower's security system as they think she is Wonder Woman because of her height and her bracelets. We see flashbacks of Batman designing the traps after the death of Barry Allen. Batman believes that there should be some form of security since the alien Agamemno had so easily allowed common criminals the ability to exchange bodies with the League. Amazo the android can absorb any League member's powers and Hal Jordan had betrayed the League already.
In Batman's files we see how he designed the traps for all League members and even reserve members. Batman also keeps it hidden from telepaths like J'onn through a hypnotic suggestion that buries the information deep in his subconscious.
The only exceptions were Big Barda and Orion because they both hail from New Genesis and Apokolips, Batman has no data on New Genesis or Apokoliptian technology.
This story is the basis for the animated movie Justice League: Doom.