- Supervillains from the DC Universe start a battle against a group of superheroes from another universe.
- Whilst en route to Stryker's Island with a "special subject," Commissioner Gordon receives word from Detective Renee Montoya that The Joker has broken into Wayne Tech. Dismissing this to focus on the task at hand, Gordon proceeds to Metropolis. Arriving at Stryker's Island, he meets with the incarcerated Lex Luthor, seeking assistance regarding a very peculiar suspect. This mysterious individual had been apprehended following a break-in at a laboratory previously owned by Professor Ivo, a colleague of Luthor. Ivo and Luthor had both taken part in the 'Amazo' Project, an android capable of stealing powers from heroes.
The mysterious individual arrives accompanied by Lex Luthor's personal bodyguard, Mercy Graves, disguised as a security guard. Mercy reveals herself to those present and successfully releases both Lex and the rookie villain from custody. The trio proceeds throughout the penitentiary, reuniting with Cheetah and Solomon Grundy along the way. The group delves further into the facility to break out Metallo, who is able to apprehend Superman following his arrival. They proceed out to the coast, followed by the newly released prisoners, where they are intercepted by the remaining members of the Justice League, sans Batman.
Meanwhile, following the Wayne Tech break-in, The Joker and Harley Quinn are captured by Batman in the Batwing. Caught in the battle between the newly released inmates and the Justice League, the Batwing crashes, and Batman is chased away by Grundy. In an attempt to flee the area, The Joker and Harley climb the Gotham City Clocktower and board the Jokercopter. Their victory is short-lived, however, as they soon crash into Lex and Mercy, landing on a nearby rooftop. Suddenly, the released inmates are all defeated with ease by a new group of individuals, calling themselves the "Justice Syndicate," who each appear to be physically similar to a member of the Justice League. Following the brief introduction, Superwoman claims the Earth is endangered due to a threat from the Justice Syndicate's planet of origin... them. Johnny Quick throws a device toward the Justice League, warping them away.
Harley Quinn watches the scene unfold as she escapes with Lex, Mercy, and The Joker. As the Justice Syndicate broadcasts a message to Earth, introducing themselves as heroes from another world temporarily replacing the Justice League as they attend to a mission in space, Harley watches, completely baffled at the lies being told. The group splits, with The Joker and Harley continuing their mission to find an object of value, starting by recruiting The Riddler, Clayface, and Scarecrow. The new trio is tasked with raiding the vault within the GCPD to acquire a "toy" for The Joker. They successfully breaks into the vault as Batgirl and Nightwing arrive to stop them. Before the two can apprehend the villains, Catwoman and Two-Face arrive and knock them unconscious. The group exit the GCPD with many of their old toys returned, but Nightwing and Batgirl catch up to them to stop the truck. In the ensuing chase, Harley is ejected from the vehicle shortly before it crashes into the Iceberg Lounge. Joined by The Penguin, the group is able to defeat Nightwing and Batgirl, though some villains are knocked unconscious in the process. Riddler, Catwoman, and Clayface manage to escape, while the others are captured by the GCPD and sent to Arkham Asylum following Owlman's arrival.
Cheetah arrives at the Hall of Doom with the rookie in tow, and meets up with Catwoman, Riddler, Clayface, and a plethora of other villains. Catwoman brings up the notion that the Justice Syndicate may not be who they say they are, so the group discuss how to reveal such an idea to the world, allowing the villains to wreak havoc. Heat Wave brings up the idea to travel to Earth-3, and Reverse-Flash mentions that they may be able to do so using The Flash's Cosmic Treadmill at S.T.A.R. Labs. Catwoman plans to track down Harley Quinn, as Riddler heard her say she saw the Justice Syndicate do something suspicious. Reverse-Flash travels to S.T.A.R. Labs alongside Heat Wave, Captain Cold, Malcolm Merlyn, and the Rookie. The group arrives at S.T.A.R. Labs to find the Cosmic Treadmill destroyed. In the process of repairing it, they run into Killer Frost and Mirror Master. Kid Flash soon arrives alongside Beast Boy and Raven in an attempt to stop the villains. The villains quickly get the upper hand in battle, whilst Reverse-Flash successfully discovers that the Justice Syndicate is actually the Crime Syndicate, evil parellels of the Justice League from Earth-3. Johnny Quick, Deathstorm, and Atomica soon arrive and help Kid Flash, Beast Boy, and Raven apprehend most of the group with only Killer Frost and the Rookie managing to escape.
Some villains head to Perry White, editor-in-chief of the Daily Planet, in an attempt to convince him of the Justice Syndicate's evil nature, but the group is quickly dismissed. Writer Kent Clarkson (the alter-ego of Ultraman) brings the group aside and suggests they find Harley Quinn for an interview, to which the villains agree, and promptly leave. Catwoman plans to check Harley's secret hideouts, while she sends Killer Frost and the Rookie to Belle Reve to see if Harley's Task Force X acquaintances know her whereabouts. With Deadshot and Captain Boomerang in tow, the newly formed group heads to the Gotham Botanical Gardens to retrieve Harley. Upon arrival, Captain Boomerang cuts some vines, sending Poison Ivy into a rage. A battle ensues, until Catwoman intervenes and they reveal their intentions to Harley, who is quickly taken away by Deathstorm and Grid, though she drops the artifact The Joker found during the Wayne Tech break-in. The group rushes to rescue Harley, and she escapes with Ivy, Deadshot, and the Rookie while Killer Frost and Catwoman hold off the Crime Syndicate. The group climbs the Galaxy Communications Tower in an attempt to reveal Harley's video to the world, but Ultraman intervenes. Despite Harley's efforts, citizens still stand with the "Justice Syndicate", who all arrive alongside Ultraman.
Meanwhile at Arkham Asylum, Lex Luthor stages a breakout for The Joker and other inmates, with the promise to meet Lex at the Hall of Doom. Joker, Captain Cold, Livewire, Reverse-Flash, Malcolm Merlyn, and Solomon Grundy promptly escape their cells and traverse throughout the Asylum. Upon gaining access to the exit, The Joker and Livewire fall down a trap door and encounter Doctor Hugo Strange. Strange releases his newest creation, a former prisoner that he transformed into an abomination dubbed the "Monster Man." The duo is able to defeat the beast shortly before Mercy Graves arrives in the Jokercopter and brings them to the Galaxy Communications Gala. With the help of Livewire, the large group of villains is able to escape from the Crime Syndicate and head toward the Hall of Doom, where all the villains reunite. Lex Luthor brings up that he traveled to LexCorp to investigate the Crime Syndicate, and discovered they're searching for a mysterious artifact. The group plans to create a team of the baddest villains around, starting with Gorilla Grodd.
Lex Luthor, Cheetah, Reverse-Flash, Heat Wave, and Captain Cold travel to Gorilla City and are met with opposition by the local gorillas. Moving forward to the throne, they find that Solovar has taken over. The group is able to help Grodd preform a coup of the throne, defeating Solovar and gaining Grodd as an ally. Grodd recruits Killer Frost, Scarecrow, and The Rookie to get Sinestro, who has been captured by the Crime Syndicate and imprisoned on Oa. The group heads to Smallville to find a way to Oa, where The Atom awaits. He's quickly defeated, and Grodd locates a slideways teleporter in storage that they use to travel to the Justice League Watchtower. The villains are able to steal a ship from the Watchtower and successfully arrive on Oa, though the ship is quickly destroyed. Meanwhile, Power Ring turns Sinestro into the Guardians of the Universe, who take time to discuss what to do with their new prisoner. Thanks to Scarecrow's fear toxin, Sinestro is released from the Green Lantern Corps' control. Power Ring, attempting to fit in with the Green Lanterns, is having trouble controlling his ring due to his lack of willpower, so he is easily overpowered by Sinestro and the others. Power Ring is mocked by the Guardians of the Universe, while the villains return to the Hall of Doom. Meanwhile, Mercy Graves discovers that the Crime Syndicate is working for a higher power, as they discuss with Kalibak about their current progress locating the unknown artifact.
With Sinestro's arrival at the Hall of Doom, a new team is formed with the goal of freeing Black Adam from his sarcophagus and recruiting him. Sinestro is joined by The Joker, Harley Quinn, and Clayface at the Gotham Museum of History as they track down Black Adam. The group successfully frees Adam moments before Billy Batson triggers security and transforms into Shazam. Superwoman soon arrives, along with Mazahs, an actual hero from Earth-3. Superwoman flees following Mazah's arrival, and a battle between heroes and villains ensues. Black Adam and Sinestro are able to defeat, and imprison, Shazam and Mazahs. Adam is hesitant to join the group at first, but with threats of imprisonment in his sarcophagus, he agrees, and the group returns to the Hall of Doom. Meanwhile, Mercy continues to spy on the Crime Syndicate, who are growing tired of playing heroes. Sea King leaves the group and travels to the Hall of Doom with a giant octopus, taking the hall underwater to Atlantis. Poison Ivy avoids the attack, as Black Manta and King Shark arrive, fearing the giant octopus. With some persuasion from Ivy, the two join the battle against the Crime Syndicate. The trio tracks down the octopus and are able to weaken it enough to save Harley, but Sea King flees deeper into the ocean with the Hall of Doom. Black Manta and King Shark give chase, and successfully defeat Sea King and return the Hall of Doom to its proper location.
With the supervillain team assembled, Lex Luthor concludes that they must act now, as the Crime Syndicate know their whereabouts. Lex, in his new Power Suit giving him the powers of Superman, travels to LexCorp with the Rookie in tow. Meeting with Sinestro, Grodd, and Adam, the group finds that they're locked out of LexCorp, but they're able to break in with ease. The group arrives to find the other villains captured, as Lex had previously warned the Crime Syndicate that they'd be coming. The villains aren't too fond of Lex's scheme, so a battle ensues, with two groups of villains fighting Grid and Deathstorm. The villains are able to defeat the two syndicate members, while the battle gives Lex enough time to hack into the Crime Syndicate's warping tech. Lex attempts to warp everyone present away, like with the Justice League, but the Rookie intervenes. The warping device malfunctions, and a new planet appears in the sky - Apokolips.
The Joker, Harley Quinn, and the Rookie are warped to Apokolips. The Joker notices what he believes to be a "party" occuring at the central area of the planet, so the trio head toward it. Upon arrival, they overhear Darkseid, ruler of Apokolips, discussing the Earth situation with his underlings; Dessad, Kalibak, and Granny Goodness. Darkseid mentions an "anti-life equation" that he plans to create using the artifact the Crime Syndicate is trying to locate. Unfortunately, the device Harley has kept from the Wayne Tech break-in starts to make noises, alerting Darkseid of their presence. Moments before Darkseid vanquishes our villains, the Justice League enters the room, and are shocked to find The Joker and Harley present. Darkseid quickly knocks Superman into space, as John Stewart arrives with the Green Lantern Corps. The remaining Justice League members retreat to the Watchtower with Joker, Harley, and the Rookie. The Justice League explains that the Anti-Life Equation will grant the user complete control over the universe. Meanwhile on Earth, the Crime Syndicate have begun telling citizens that the arrival of Apokolips means the Justice League failed their mission, and have turned evil.
Wonder Woman, Cyborg, and Harley Quinn travel to Themyscira, where they find Granny Goodness and Virman Vundabar have taken control of the Amazonian forces. The trio successfully defeat the forces of Apokolips and free the Amazons, gaining their trust for when they're needed in the upcoming battle against Darkseid. Meanwhile, Batman, Joker, and the Flash travel to Nanda Parbat to recruit Ra's al Ghul and Deathstroke. Deathstroke delays the group as Ra's tests their dedication, and eventually the duo agrees to join the cause. Having successfully located Superman on Dinosaur Island, Aquaman, Hal Jordan, and the Rookie head there and are confronted by Kalibak, general of Darkseid's army. Following Kalibak's retreat, the trio frees Superman, only to find that Darkseid himself is descending upon Earth. Darkseid introduces himself to Earth and fakes a brawl with the Crime Syndicate to further convince Earth that they're heroes. Batman decides that they're only one thing to do at this point - the Justice League must team up with the Legion of Doom.
Clark Kent calls a panic-stricken Lois Lane, who has been following the story since the beginning, and tells her that she needs to meet with Superman at an unspecified location. Meanwhile, the Justice League team up with the Legion of Doom to act as though they truly have become evil, playing along with the Crime Syndicate's game. First, The Flash and Reverse-Flash chase down Johnny Quick and Atomica, and interrogate them for information about Darkseid's Plan. Johnny Quick says that Darkseid is looking for a "mother box", which contains the Anti-Life Equation that Darkseid is after. Unknown to Johnny Quick, Lois Lane filmed the entire interaction, and reveals to the world that the Crime Syndicate is working for Darkseid. Heroes and Villains alike storm the Hall of Justice to defeat the Crime Syndicate once and for all. The Justice League battle their evil counterparts, with assists from the Legion of Doom along the way. The Crime Syndicate is defeated and, thanks to the Rookie, they're sent back to Earth-3. In the process, the Rookie absorbs the power in Harley's item, revealed to be the motherbox saught by Darkseid. Back on Apokolips, as the battle with the Green Lantern Corps continues, Darkseid watches as Batman reveals the location of the motherbox.
Batman and Robin head to Wayne-Tech to investigate the motherbox, which Batman is using to distract the forces of Apokolips while Superman finds a way to send the planet back to where it came from. The dynamic duo arrive at Wayne Tech and are attacked by Steppenwolf, who quickly realizes that the anti-life equation is located within the Rookie. The Rookie flees into Wayne Tower while Steppenwolf is kept busy outside, though Parademons are soon able to capture the Rookie, who is then taken by Steppenwolf. Batman and Catwoman give chase on the Gotham City Monorail, and successfully knock Steppenwolf off using the Batwing. Unfortunately, Darkseid arrives, takes the Rookie, and warps the monorail, with Batman and Catwoman still on it, high above Metropolis. Before hitting the ground, Lex Luthor, still in his Power Suit, arrives and saves them. On their way to the ground, Batman and Catwoman explain the situation to Lex, who is worried about "his" Rookie. The Legion of Doom arrives, initially angry at Lex for his attempted betrayal, but their anger quickly subsides once they realize they all would've done the same thing in his place.
The Justice League and Legion of Doom warp to Apokolips to make one final stand against Darkseid and save the Rookie, as Lex has a plan to send Apokolips back to where it came from. Upon arrival, Desaad holds off the group while Darkseid attempts to finish extracting the anti-life equation from the Rookie, but the heroes and villains quickly defeat Desaad's contraptions, making Darkseid fight the group himself. The battle proves useless, however, as Darkseid is able to retrieve the full anti-life equation from the Rookie. The group retrieves the Rookie, as Lex retrieves many other allies. Darkseid, now the most powerful being in the universe, sends the group to an arena of his creation where they make one last stand against him. The group is able to defeat the forces of Apokolips, leaving Darkseid baffled, as he should have knowledge of everything in the universe. With that being said, Batman deduces that the Rookie is actually from Earth-3, like the Crime Syndicate, so the Rookie is able to turn the forces of Apokolips good due to the power of the motherbox mixing with his Earth-3 energy. With Darkseid neutralized, Lex threatens to send Apokolips back with everyone still on it, leaving him to have full power over the Earth, and he does.
Back on Earth, Lex demands to be made emperor, but citizens say: "Boooo! Boo to you! Boooo!" Angrily. Lex reminds the group present, including Lois Lane, Jimmy Olsen, and Commissioner Gordon, that they don't have a choice - all of Earth's heroes and villains have been sent to Apokolips. Suddenly, the group returns from the distant planet, as the Rookie was able to teleport them back to Earth, to which Lex remarks he was telling humanity of their "sacrifice". They attempt to arrest Lex, who deflects his situation to the Rookie. Both sides acknowledge the Rookie's importance in defeating the forces of Apokolips, and the Rookie is given a choice to either permanently join the Heroes, or remain a Villain.- If the Rookie chooses to become a Hero, Lex is hurt by the decision, though Joker reminds him that he tried to send him to the other side of the universe. The two fight, as Livewire teleports them all away, except Captain Cold who awkwardly runs off. Afterwards, the group head off to fight crime anyway.
- If the Rookie chooses to remain a Villain, the Joker insists that he becomes the leader of the Legion of Doom, as Lex can no longer be trusted. Lex angrily states that they'll discuss it back at the Hall of Doom, as the Rookie teleports them away.
Meanwhile on Apokolips, a new threat arrives, disgusted by Darkseid's newfound goodness.
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