Issue 1 begins with a montage of the Society members (Calculator, Talia Al Ghul, Black Adam, Deathstroke, Dr Psycho and Lex Luthor) propositioning various villains, offering them the chance to join the Society. In the first four pages, around twenty villains are shown joining up; the first to refuse them is Catman. Dr Psycho and Talia are surprised at his refusal, though Talia is also respectful of Catman’s obvious regeneration: he’s changed from a something of a joke to a man who reminds her of Batman. When they report back to the Society, Calculator describes Catman as a “third-rate never was” while Deathstroke compares him to Ambush Bug and Crazy Quilt. Despite the Society’s calls for Catman to be made an example of, Luthor decides to leave him alone.
In the Amazon forest, the group known as The Secret Six (Scandal, Deadshot, Cheshire, Parademon, Ragdoll II and The Fiddler) are attacked while placing a “lozenge” in the ground on orders of someone known as Mockingbird. Due to poor performance in the mission, The Fiddler is killed by Deadshot. In order to make up their numbers, Deadshot and Scandal travel to Africa and ask Catman to join them who agrees as the Society had Deathstroke kill the pride of lions Catman lived with. Before he leaves with them, he hands a letter addressed to Oliver Queen (Green Arrow) to the barman to mail.
They return to the Six’s headquarters, the House Of Secrets, where, via a video feed on a big screen, Mockingbird tells them why he’s drawn them together: to overcome their previous failures against the heroes and strike at the Society at the same time. To ensure their compliance, he tells them he has taken what each of them cannot bear to lose and made it his own. Success with The Secret Six, however, means that each of them will own a continent.
Issue 2 starts with Deadshot and Catman talking in the kitchen with Catman suspecting that Mockingbird may actually be one of the Six, a reference to previous incarnations of The Secret Six where Mockingbird was a member of the team. Their conversation is overheard by Cheshire, while Scandal e-mails someone referred to as her “Beloved.” Parademon snores in his sleep, forcing Ragdoll, who shares his room, to wrap a pillow around his own head.
A mission from Mockingbird interrupts the night; a raid on a cargo ship moored in Gotham holding Thanagarian weapons intended for the Society. While the Six plot their attack, they are unknowingly heard by the Society who have a bug on their plane.
The Six arrive in the middle of a rainstorm and, upon boarding the boat, find it to be empty. As they return to Scandal who had remained behind as a coordinator, they are ambushed by over a dozen villains working under the command of the Society. While Catman holds off the villains, the other members of the Six attempt to escape. They are captured, however, and Catman eventually wakes strapped to a torture chair of the Crime Doctor who wants to know the identity of Mockingbird.
Issue 3 begins with the Six each taking a turn in the Crime Doctor’s chair, an hour at a time. None of them fare well until the Doctor gets to the Parademon who, having been raised on Apokolips, merely laughs at during his torture.
While the Six are tortured, their guards play a game of Metropolopoly (which features such landmarks as Suicide Slum and the Lexcorp Tower), though Knockout alone feels uncomfortable with the screaming. One of the Society’s leaders, Black Adam, deplores the use of torture but is convinced by Luthor of its necessity; Luthor reveals the “lozenge” placed in the Amazon by the Six in issue 1. According to him it is a bio-explosive which devastates an area of two thousand square miles. He tells Adam that they have found another within the borders of Khandaq, the country Adam rules.
As Scandal takes her turn in the chair, some of the Six tell each other what Mockingbird has on them that forces them to work with him. Catman persuades Cheshire to study the electronic collars they all wear which, if removed, will inject them with poison. With this information, Catman takes Deadshot’s turn and tricks the Crime Doctor into shorting out the collar, allowing him to break free. He makes Captain Nazi deactivate the collars on the others and takes them their clothes and equipment.
The Six break out and attack the guards and, after subduing them, Deadshot kills Hyena as a message to the Society.
Issue 4 starts with the new Jack of the Royal Flush Gang telling the warden of the prison he is held in that, soon, a message will come for the warden to open the gates. Not just of the one prison, but of hundreds across the country. He convinces him that members of the Society have been in his house, an implicit threat against his family.
In Brasilia, the Six are on a misson to disrupt the Society’s plans by destroying a complex of his. While they do that, the Society has a meeting in Gotham where Luthor learns from Talia that, since the Six escaped, their recruitment drive has been less than successful. The scene is notable, though, for the inclusion of a villainous version of one of the DCU’s most ineffective super-teams, the Inferior Five. Luthor and Talia are alerted to the break-in at the Brasilia compound.
In Brasilia, the Six infiltrate the compound, forcing Luthor to send Black Adam and a strike force to protect it. The current guardians, HIVE agents controlled (appropriately) by the Queen Bee, are massacred by the Six while Scandal downloads their mainframe. She finds out that the Society are planning to mindwipe all the superheroes of the world.
They find the powersource (Firestorm and another person held prisoner and used as living batteries – Firestorm was captured by the Society in Firestorm #16) just as Black Adam and the Royal Flush Gang arrive. Rather than stay and fight, Deadshot convinces the Six to free Firestorm and let him deal with the Society while the Six retreat.
Back at the House of Secrets, Catman tells Cheshire a rough version of his origin and how he changed himself from a joke to a man. In return, Cheshire tells him she wants him to give her a baby.
As Scandal finds encrypted data from the Society, Luthor has a meeting with Vandal Savage which is interrupted by the arrival of the Fearsome Five. Luthor gives them a specific target to find before Savage leaves, resigning from the Society.
In deep space, Sinestro is shown capturing Lady Quark, the last survivor of pre-COIE Earth 6.
The Society heads, meanwhile, vote to take down the Six once and for all with all but Luthor voting for the attack. At the end of the meeting, the Fearsome Five return with their prisoner: Pariah, the harbinger of doom who played a key role in Crisis on Infinite Earths. Pariah warns Luthor “You think you’re this planet’s apex predator. But there’s another. And you won’t survive his coming.”
Back at the House of Secrets, Mockingbird calls a meeting to inform the Six he knows of their attempt to discover his identity and threatens their loved ones. Catman makes him a counter offer of sending the Six against the Society. Following the meeting, Catman confronts Deadshot, accusing him of being the one who killed the pride of lions Catman had lived with, which Deadshot admits. Before the fight can continue, however, the perimeter alarm sounds. Cheshire had betrayed them by leading the Society to their door. Even if Mockingbird killed her daughter, as he threatened, she was now pregnant with Catman’s child so had nothing to lose.
Issue 6 begins with the final assault by the Society on the House of Secrets. Within, Deadshot plans to kill Cheshire for her betrayal but is stopped by Catman who, while not totally convinced she is pregnant with his child, isn’t convinced she’s not. Catman convinces Deadshot to allow Cheshire to leave. As she leaves the house, however, Deathstroke shoots her.
At the Society’s tower in Gotham, Luthor talks with the captured Pariah who reveals that there is another Luthor. Luthor, however, isn’t impressed because he is the other Luthor; the other one is using the name Mockingbird. Pariah tells him that the Six know of his plans to mindwipe the heroes, but Luthor informs him that he has something more interesting planned. In order to keep Pariah quiet, Luthor kills him.
Mokingbird, now revealed as Lex Luthor, abandons his submarine hideout while wearing the green and purple Kryptonian battlesuit and swears to find the Society’s Luthor whom he calls a pretender.
In the House, the Six battle against the Society’s soldiers with the Society losing several members. As Talia and Scandal fight, Scandal reveals that she had a mole in the Society’s ranks all along – her “Beloved” who is revealed to be Knockout. Deadshot confronts Deathstroke in an attempt to repay his debt to Catman over the killing of his pride.
Catman, Ragdoll and Parademon are cornered by Black Adam and others. Rather than fight to the death, Parademon tells the other two to leave as he self-destructs his Mother Boxes, destroying a large part of the house.
As the battle continues, Luthor is forced to call a retreat by Vandal Savage, Scandal’s father. Mockingbird contacts Scandal to admit to never having planned to harm their loved ones.
Some time later, Catman and Deadshot meet with Green Arrow and tell him of the Society’s plan to mindwipe the heroes. Catman lays the blame for the whole Society’s formation at the feet of the heroes who mindwiped Dr Light in Identity Crisis, including Green Arrow. He and Deadshot leave, trying to decide whether to be good guys or not.
The events of the Villains United Special take place directly before the start of Infinite Crisis #7. It starts with the wardens of prisons across the globe receiving word from Society members that the time will come to open the gates and let the villains loose.
The reminaing members of the Six, with Knockout in place of the deceased Parademon, meet at a diner to discuss what they are going to do – as Deadshot puts it, should they be “good or bad, white meat or dark”?
The Society meet – with Luthor attending as a hologram – and begin the operation to free as many prisoners from as many prisons as they can. Oracle attempts to coordinate the movements of the heroes in an attempt to prevent as many escapes as she can. She contacts as many heroes as she can; with the big guns attacking Alex Luthor’s tower, she resorts to heroes such as El Diablo, Manhunter, Agent Liberty as well as more familiar heroes like Arsenal and Black Canary. With the aid of J’onn J’onnz’s telepathic link, Oracle is able to contact almost every hero in existence.
The Six masquerade as Society members to apparently rescue Scarecrow and Amos Fortune; though they accept the offer of a ride by helicopter, they are quickly suspicious. A careless remark by Fortune ends with him being thrown from the helicopter. Scarecrow unleashes his fear gas but, with the application of pepper spray to his own eyes, Catman is able to overcome it and wrest from him the destination of all the escapees: Metropolis.
Green Arrow gets the word from Catman and lets J’onn know; every available hero makes their way to Superman’s city where Dr Psycho introduces the Society’s big gun: Doomsday. As the fight that leads into Infinite Crisis #7 begins, the Six fly away, reluctant to be forced to be either good guys or bad.