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Trinity War is a major crossover event in the New 52 surrounding the Trinity of Sin. It stars the Justice League, Justice League of America, Justice League Dark against the Secret Society of Super-Villains and the Crime Syndicate.
Madame Xanadu, who can see the future, has a vision of a conflict that will end with disaster. She shouts that she knows what "Trinity" is, and that they are coming. However, before she can warn anyone, she is kidnapped by Plastique of the Secret Society.
Amanda Waller has built the Justice League of America, A.R.G.U.S.' safeguard against the Justice League, should they go rogue. Her latest asset, Dr. Arthur Light, is meant to counter Firestorm. However, he is only trained as a scientist and doesn't know the origin of his powers. What is more, he has a close relationship with his wife, telling her everything, so Waller has to threaten to wipe her memory to keep him in line.
At the Justice League Watchtower, which has crash landed into the Rhode Island shore, Cyborg worries about gaps in their cyber-security while Atom, who is secretly acting as a mole on the Justice League for Amanda Waller, finds a Justice League chess set with the Superman piece missing.
At Belle Reve, Pandora tracks down Superman and asks him to help her open Pandora's Box. Despite disbelief, he agrees, only to be turned into a villain while he is holding the box. Wonder Woman and Pandora manage to bring him down, but Pandora moves on.
The Justice League gathers to save Shazam, who has broken the no-fly area over Khandaq to scatter Black Adam's ashes. Through her mole, Atom, Amanda Waller learns of this and sends the JLA to reign in the Justice League.
After arriving in Khandaq, Shazam faces the army, then fights the Justice League when they try to stop him. The JLA shows up to get them all to leave, and tempers rise, but Superman and Dr Light both try to calm the situation down. This ends when it appears that Superman kills Dr. Light. The two teams clash against each other in rage. This news appears to a few people: the Phantom Stranger, who wants to save lives; the Outsider, who wants to steer the Secret Society of Super-Villains and Pandora to his mysterious endgame, and the Question, who just wants to find the party ultimately responsible.
In the middle of the fight, Martian Manhunter tries to scan Superman's mind for influence, before getting dragged into a brawl with Flash and Vibe. Superman ends the fight by knocking everyone aside and demanding to be taken into custody, frightened what could happen if he was not in control. At A.R.G.U.S. HQ, Steve Trevor confronts Amanda Waller, who says that she did not create the situation but intends to use it for political advantage, even though it frightens her. When the mass of heroes arrive, she pulls Firestorm aside and asks him to make her some kryptonite. Wonder Woman confronts Steve Trevor and complains that he should have contacted her - this is the first time they have spoken since the aftermath of the Graves incident, and she first found out about the JLA from the television.
In the holding cell, Superman feels sick. After some pushing, Batman tells Superman about Dr Light and his family. He says Cyborg and Martian Manhunter are overseeing the autopsy in hopes of proving Superman's innocence. Wonder Woman enters the cell, and tells them about Pandora and her box. Batman insists that a scientific method will provide the answers, while Wonder Woman holds to magic. She leaves to gets answer from Hephaestus. Under the Lasso of Truth, the smith-god tells her that the gods used Pandora to open the box because they had no idea what was inside it; the box was not of a divine origin. As she leaves, Hephaestus advises her to destroy the box if she gets the chance. Needing help, she calls on Justice League Dark, who are searching Madame Xanadu's home for clues to her whereabouts.
Disguised as Steve Trevor, the Question enters Superman's cell and removes his shackles. Unmasking himself, he asks Superman to help him investigate the Secret Society to get justice for Dr Light.
Zatanna tells the heroes that she cannot help them magically with the autopsy. The Phantom Stranger arrives and cryptically warns them that if Wonder Woman catches Pandora, it will spell doom. Firestorm stays behind but the rest of the heroes head to the House of Mystery to head them off. Superman tries to join them with a press clipping from the Question, but A.R.G.U.S. agents move to stop him. Green Arrow blows out a wall and the heroes escape. During the escape, Superman has trouble controlling his heat vision again.
The Question and Superman lead a group of the heroes after Doctor Psycho, a Secret Society stringer and telepath who was sighted in Khandaq. The other heroes go to the House of Mystery, where the Phantom Stranger takes Batman, Deadman and Katana to interrogate the soul of Dr Light in Heaven, while Wonder Woman recruits a host of heroes to help her track Pandora to the Belle Reve prison. Constantine lures Shazam away by explaining he knows where his family is, and the remaining heroes are left trying to break back into the House of Mystery to help the Phantom Stranger.
At a secret location, the Outsider confronts Madame Xanadu and tells her that events are proceeding as he planned: Superman and the Question are running in circles, while Wonder Woman, Batman and the Phantom Stranger are directly helping him by isolating Pandora. Madame Xanadu mocks him, saying she doesn't need precognition to know the Justice League will stop him. The Outsider merely smiles, explaining that he has already won: he has a mole on the Justice League.
Superman's team track Doctor Psycho to a sewer in Pittsburgh, where he admits that he was sent to Khandaq but he wasn't involved in the incident. At this point, Atom comes clean, admitting that she is Waller's mole on the Justice League. The team questions whether Amanda Waller is actually responsible for this whole disaster, and goes confront her. However, when they get there, A.R.G.U.S. HQ explodes thanks to a bomb Plastique set, made from the corpse of Dr Light.
At the House of Mystery, the leftover heroes try to force their way in, but succeed when Catwoman convinces the House to let them in. They arrive just in time to see Phantom Stranger push the other three to safety out of a magic mirror, then warn everyone to find Madame Xanadu as she knows the truth about the box. Then he vanishes. The Phantom Stranger has gone to Heaven and died.
Pandora breaks into Lex Luthor's cell and asks him to help her open the box. Before he can touch the box, Wonder Woman's group arrives, and she grabs the box, but is instantly corrupted by it and tries to kill everyone else in the room.
She is stopped by the sudden arrival of Shazam, who takes the box from her but is himself corrupted - and because of his connection to the magic of Earth, this results in danger-warnings to most of the world's magical heroes and, most worryingly, to Doctor Fate of Earth 2. Despite Zatanna's efforts to solve the problem with magic, the day is actually saved by John Constantine. As he is already corrupted, the box has no pure good or evil to use to convert him. He teleports himself and Zatanna to the Temple of Hephaestus in Greece, where they find Madame Xanadu is being held. Deadman is able to direct Batman's team to that location. Madame Xanadu tells them that Pandora was wrong: the box is not a prison, but a doorway.
At the battered A.R.G.U.S. HQ, Amanda Waller admits that she had nothing to do with the murder of Dr Light or the framing of Superman. Firestorm tells the rest of them that she asked him to make kryptonite.
In the shadows of the Temple, the Outsider thinks of his origin: how five years ago, the passage of Darkseid weakened the walls between this world and others, and his master's allies tried to come here. They failed, but he made it through with one ally. He has been working ever since, recruiting enemies of the Justice League, researching Pandora's Box, and trying to plant a mole on the Justice League.
The rest of the heroes arrive at the temple. Constantine realizes that the box puts evil thoughts in people's heads, just as the heroes start to fight each other. Batman takes the box, but starts fighting Superman. Wonder Woman ends the fight by knocking Batman unconscious, causing the box to go dormant. She then sees Superman is still ill, proving her theory that the Box was making him weak and evil wrong. Firestorm realizes that Superman is undergoing kryptonite poisoning, and Element Woman goes into his bloodstream, discovering a sliver of kryptonite pressing on an area of his brain.
And then the final part of the mystery comes out: Atom planted the sliver in Superman's brain just after they got to Khandaq. It has been pressing on his brain ever since, causing him to lose control of his powers. She is the Outsider's mole. She has however been building a friend. On a word of command, she brings Cyborg's prosthetics under the command of an intelligent computer virus called Grid, and they separate from his human body. The Outsider steps from the shadows and picks up the box. He explains that the Box is the product of science from his world, and that since his soul is pure evil, he can open the doorway. As the box is consumed by the doorway to his master, Madame Xanadu explains the truth. "Trinity" was never about the three Leagues or the Trinity of Sin, or even Superman, Batman and Wonder Woman. It was about the world that is the stronghold of evil. It was about Earth 3.
The Crime Syndicate, the wicked rulers of Earth 3, emerge from the doorway, though Sea King dies in the crossing. Owlman commends the Outsider for his service. Atom goes to join them and reveals she was one of them, going by the name Atomica. As Superwoman drags a hooded prisoner through from their world, the rest of the team jumps the heroes, who are worrying over Superman, and shout that this world is theirs now.