The Trinity is summoned to the Rock of Eternity to be judged by the Circle of Eternity for their crimes against humanity. The Phantom Stranger pleads for forgiveness, arguing that he who he betrayed would forgive him. However, he is beyond forgiveness, and is sentenced to walk the Earth as a stranger to man, and as a witness to what greed is capable of, while his hair and eyes turn white, and the 'thirty pieces of silver', burn themselves into his flesh. The Question defies the wizards, saying that if they do not kill him, he will rise to power again. However, he is sentenced to forget his name as everyone else will; to forever question his identity and forever search for answers that he will never find. His face then becomes blank, and he is mute. Pandora is last to be sentenced, but is sorrowful, not realizing what she has done. She appears truly repentant, but is still sentenced to an eternity of loneliness, pain and being deemed evil. And so the Trinity of Sin were created.
The members of the Trinity continue to walk the earth but they have begun to be more than just observers. The Question is still searching for answers and has been dealing out vigilante justice in places like Hub City and believes that the Phantom Stranger and Pandora hold the answers he seeks. The Phantom Stranger has been wandering the earth and following the voice of a Higher Power to take interest in certain people. The Stranger must then betray these people in order to remove one of the thirty pieces of silver from around his neck. These betrayals have resulted in the creation of the Spectre and have stopped an invasion by the forces of the demon Trigon. At the same time, however, the Stranger tries to remove himself from his curse and has started a family and has a wife and two children. But he cannot find peace and his life is constantly interrupted by different people and beings from his life as the Stranger, including Dr. Terrence Thirteen. Pandora has spent her wanderings trying to figure out what she had done to deserve her punishment and how she could set it right. She determines that she must put back what she had released from the box and begins by stealing it from the Black Room at A.R.G.U.S..
Seeds of War
Pandora quickly discovers that she can no longer open the box to put back what she had released. At the same time she is visited by the Wizard who cursed her who tells her that she cannot put back what was released but there is still power within the box to set things right. He tells her that only the strongest of heart or the darkest can open it. The Wizard then asks for her forgiveness for the Circle's harsh punishment of her because she did not deserve it. The other sinners deserved their punishment but she was just curious. Then the Wizard vanishes after having passed the last of his power to a new champion.
The Phantom Stranger continues to try to live a normal life but is visited by Pandora who asks for his help in finding the one who can open the box. The Stranger refuses though and says that he will do everything in his power to stop her from releasing anything else from the box. Pandora chastises him for trying to live a normal life with the curse that he bears and warns him that if he tries to interfere in her plans then she will reveal his true identity to all of those he cares about. Realizing the inevitable the Stranger travels to Nanda Parbat to warn John Constantine that war is coming between the three and that it is time for him to choose a side. However, Constantine, and the rest of the Justice League Dark, refuse to take part and instead try to convince the Stranger to join their team, but the Stranger, in turn, refuses them.
In the meantime, the Stranger's family is kidnapped. Pandora appears to let him know that she had nothing to do with the his family's disappearance. The Stranger then confronts the Spectre, believing him to be responsible for the kidnapping. But yet again he finds a dead end. At the same time, Dr. Thirteen is confronted by the Question who asks him what it would take for him to betray the Stranger. Dr. Thirteen then calls the Stranger and tells him that he will find information about his family if he visits a casino in Las Vegas. At the casino the Stranger runs into the Sons of Trigon who are playing a game of high stakes poker with the dealer being Lady Luck. The Stranger joins the game with the hope of finding more information about his family. With the unexpected help of Deadman the Stranger wins the game but makes enemies of the Sons of Trigon who also know nothing about his family. Then the Stranger receives another call from Dr. Thirteen who, under the guidance of the Question, urgently tells the Stranger that he needs to come back to his lab.
After the Stranger deals with another mission given to him by the Presence he arrives at Thirteen's lab. The doctor seems a little unsettled by something and then the Question reveals himself. The Stranger is very hostile towards the Question and urges Thirteen to help him defeat the faceless man. However, the Question tells the Stranger that he cannot best him and that the Stranger must be killed. Suddenly Thirteen stabs the Stranger from behind with the Spear of Destiny. The Question then tells the Stranger to "just shut up and die".
The Phantom Stranger is mysteriously left on the doorstep of the Justice League Dark where he is saved by the Nightmare Nurse. While "unconscious" the Stranger discovers that his family has been taken by the Sin Eater who turns out to be an old enemy of the Stranger he had believed long dead. The Stranger discovers that his family has been hidden in Hell and while he goes after them Dr. Thirteen and the Question believe he is still dead. Thirteen is visibly distraught by what he has done but the Question believes the world is better off without the Stranger who was a menace to everyone he met.
But as the Stranger finally reaches the end of his journey to find his missing family, the Question has one last task for Dr. Thirteen. At the same time, the third member of the Trinity sets her sights on Superman, who she believes is the one who can reopen the box and help her put an end to the Seven Deadly Sins she released all those eons ago.
War finally breaks about between the Justice League and the Justice League of America. At the same time, Pandora is searching for the one who can help her open the box and put back the Seven Deadly Sins after discovering that Superman was too human to withstand the temptations of the box. Standing by the graves of Superman's adopted parents, the Phantom Stranger decides it is time for him to get involved in the war. And piecing together the puzzle is the Question who is looking for the answers to who is trying to impute Superman. Disguised as Steve Trevor, the Question sneaks into the ARGUS headquarters and frees Superman asking him if he wants to find out who really killed Dr. Light. Meanwhile, Wonder Woman seeks out the Justice League Dark in order to find Pandora whom she believes is responsible for Superman losing control. But the Phantom Stranger believes only evil can come from Pandora and her box so he turns to the other two Leagues to help him stop Pandora from being reached.
New lines are drawn as members of the Justice League and the JLA help the Question and Superman escape ARGUS to go after the villain known as Dr. Psycho whom they believe may be responsible for what is happening to Superman. Then Batman and Wonder Woman are at odds on what to do about Pandora and her box. Members of the Leagues begin switching sides as the Justice League Dark and members of the other two Leagues decide to help Wonder Woman find Pandora in order to help Superman while the rest of the members of the Leagues side with Batman and the Phantom Stranger who not only want to prevent the box from ever being opened again but also plan on seeking out Dr. Light in the afterlife to see if he can give any clues as to what happened.
Meanwhile, Pandora stands alone as she changes her strategy from trying to find the purest of heart to trying to find the darkest of heart. Taking advantage of the heroes' distraction, the Secret Society sends Signalman, Giganta, and Vandal Savage to find Pandora and take the box from her. However, when Pandora discovers that Savage is not dark enough of heart to open the box she says he is useless to her and escapes from the Society.
In an attempt to learn more about what happened just before Dr. Light was killed, the Phantom Stranger leads a team consisting of Batman, Deadman, and Katana into Heaven to talk with Light himself. After passing through "Heaven's Basement" and avoiding being drawn into their own personal heavens, the team finally reaches Light. Unfortunately he doesn't remember much of what happened and just after giving the Stranger something to pass on to Light's family a group of angels appears lead by the angel Zauriel. Zauriel tells the Stranger he was warned about returning to Heaven and trying to take another soul back to the world of the living. Zauriel sends Batman, Deadman, and Katana back to earth and after putting Light back into his own heaven he turns to the Stranger to deal out his punishment. Then, with his flaming sword, Zauriel erases the Phantom Stranger from existence.
After discovering that Vandal Savage was of no use to her, Pandora decides to seek out another who may be the darkest of heart, Lex Luthor. Meanwhile, the Question and his group find Dr. Psycho and interrogate him about what happened to Superman. Unfortunately Dr. Psycho claims that the Secret Society wet him up and that he had nothing to do with the murder of Dr. Light. So, the group decides to return to ARGUS to question Amanda Waller about her having created the JLA as a response to the Justice League. Batman, Deadman, and Katana find themselves back in the House of Mystery wondering what just happened. Suddenly they receive a vision of the Phantom Stranger telling them that he can save them but not himself and tells them to find Madame Xanadu. He tells them that she is alive and she knows what the box really is. The Stranger says that they have all been tricked but is wiped from existence before he has a chance to tell them how or by whom.
At Lex Luthor's prison, Pandora approaches him and tells him to open the box. But before he has a chance, Pandora is caught in Wonder Woman's lasso. They all begin to fight over the box until Wonder Woman finally gets a hold of it. But when she does, its power possesses her and she begins to fight with the rest of the heroes. Back at ARGUS, the Question's group approaches Amanda Waller while unknown to them Plastique from the Secret Society is in the morgue doing something to the body of Dr. Light. Suddenly there is a massive explosion, destroying ARGUS and leaving the status of the Question and his group uncertain.
All three Leagues track the box to Athens where they all meet up. Once in the presence of the box, however, it begins to corrupt them and they fight amongst themselves to get the box. The Question attacks Pandora wanting to know what will happen if he opens the box and if it will give him the answer to who he is. Pandora says it will make him more dangerous than the box itself. In the end the box is opened by the Outsider as a doorway to Earth-3 allowing the Crime Syndicate of America to pass through. Pandora does not understand, as she has always thought the box was the prison that held the Seven Deadly Sins. Madame Xanadu tells her that the Trinity in Trinity War was not about the Trinity of Sin but about the number 3 as in Earth-3. The Crime Syndicate then announce their plan to take over this new world and attack the Justice Leagues.
Pandora and the Question each somehow survive the Syndicate's attack and the Presence sees fit to bring the Phantom Stranger back into existence. Each member of the Trinity now seeks some new mission. Pandora, having learned that her box wasn't a prison at all but a doorway, seeks answers and goes looking for the Outsider, the one man who knows more about the box than she does. The Stranger continues to wander, saving Dr. Thirteen in the process and delivering a gift to the family of Dr. Light as he promised in Heaven. However, he later learns that Light gave him another gift when he receives a vision of his true purpose. The Question, after learning that the Stranger survived his last attack, seeks to carry out his vengeance and it is revealed why the Question hates the Stranger and Pandora so much, seeing himself as an innocent victim, tied to the world's most evil sinners not even knowing his own identity or his crime. But someone has different plans for the Trinity. Suddenly all three are transported back to the Rock of Eternity where Constantine, Nightmare Nurse, and Swamp Thing are waiting for them. Constantine tells them that he needs their help in killing evil.