Lego DC Super-Villains

Following the recent capture of an individual (dubbed "The Rookie"), Commissioner Gordon oversees their transfer to Stryker's Island in Metropolis. Enlisting the aid of the incarcerated Lex Luthor, Gordon reveals that the Rookie gained the ability to absorb superpowers and offers Luthor a reduction in his prison sentence in exchange for monitoring the new villain's powers. Before Luthor agrees, his personal bodyguard, Mercy Graves, arrives and helps break him and the Rookie out, alongside a number of other villains in the prison including Cheetah, Solomon Grundy, and Metallo. As they prepare to make their escape, the Justice League arrives to intercept them. Meanwhile, the Joker and Harley Quinn break into Wayne Tech, stealing several items, but they are forced to escape when Batman arrives to stop them. Reunited with Luthor's band of villains, the group find themselves defeated by another superhero team from a parallel Earth, called the "Justice Syndicate", with only the Rookie and Cheetah escaping. Following their swift victory, the Syndicate promptly warp the Justice League away, which Harley witnesses before being forced to escape with Luthor and Joker.

The Syndicate proclaim themselves as the League's replacements from Earth-Three, standing in for them while their counterparts are off-world on a secret mission. In the meantime, Joker leads Scarecrow, Clayface, and the Riddler, on a raid of the GCPD Headquarters, contending with Nightwing and Batgirl along the way. During their escape, Harley is accidentally lost, while the rest of the group encounters Catwoman, Penguin, and Two-Face, with Catwoman noticing Batman's counterpart Owlman acting differently for a superhero. Luthor and the villains reunite at the Hall of Doom and begin to suspect the Syndicate is not what they claim to be, prompting the Rookie, Captain Cold, Reverse-Flash, Heat Wave, and Merlyn to seek out Flash's Cosmic Treadmill at S.T.A.R. Labs in order to visit the Syndicate's world, where they discover that they are actually the Crime Syndicate – a team of villainous counterparts of the Justice League. After their discovery, the villains run into Killer Frost and Mirror Master, before being attacked by the Teen Titans, consisting of Beast Boy, Raven and Kid Flash. The villains overpower the Titans until the Syndicate's Johnny Quick, Deathstorm, and Atomica rescue the Titans and defeat the villains, except for Killer Frost and the Rookie, who escape and return to the Legion of Doom. Upon their return, Frost and the Rookie free Captain Boomerang and Deadshot from Belle Reve and recruit them to help them find Harley Quinn, eventually finding her with Poison Ivy.

Without Harley's evidence of the Syndicate's true nature, the Legion opt to meet Clark Kent's replacement at the Daily Planet, Kent Clarkson, for help in exposing the group. Unaware that Clarkson is the alter ego of the Syndicate's Superman counterpart Ultraman, the villains give the Syndicate the means to discredit Harley's eyewitness account. After Luthor helps rescue Joker and many other inmates, including Livewire, from Arkham Asylum, he reveals that he had been spying on the Syndicate's activities. Learning that they are searching for something on Earth, using their role as superheroes to gain free access to every lab and military base on the planet, Luthor reveals the object sought after could spell doom for Earth and themselves. Deciding to take up the job of saving (and then taking over) the Earth in the League's absence, Luthor begins a hunt for more powerful villains for the Legion. The villains recruit Gorilla Grodd after helping him reclaim control of Gorilla City, Sinestro after saving him from the Green Lanter Corps (where they also defeat the Syndicate's Power Ring), and Black Adam after freeing him from a sarcophagus (facing Shazam and his Earth-Three counterpart, Mazahs, in the process). The Syndicate's Sea King attempts to put a stop to them by attacking the Hall of Doom but is defeated by Black Manta, King Shark, and Poison Ivy. After Sea King's defeat, the villains regroup and launch an attack on the Crime Syndicate on top of LexCorp.

Luthor suddenly betrays everyone to the Syndicate and plans to use the Syndicate's technology to be rid of them all in order to rule the Earth alone. However, while Luthor succeeds in teleporting everyone away, he also ends up bringing Apokolips right next to Earth. As the Syndicate tries to keep Earth's people calm, Joker, Harley and the Rookie wake up on Apokolips and find themselves encountering Darkseid, the Syndicate's secret master, who ordered them to search Earth for the last piece of the Anti-Life Equation. As Darkseid discovers them, the Justice League show up, aided by the Green Lantern Corps. As they start fighting Darkseid's forces, the League and the trio of villains escape, but lose Superman in the process. The Syndicate tries to trick the people of Earth that the League became villains, thus prompting the League to form an alliance with the Legion of Doom to expose them and stop Darkseid. However, they first need to recover Superman and recruit several additional allies for their upcoming fight against Darkseid's forces: Wonder Woman, Cyborg and Harley travel to Themyscira and recruit the Amazons; Batman, Flash and Joker travel to Nanda Parbat and recruit Deathstroke and the League of Shadows; and Green Lantern, Aquaman and the Rookie arrive on Dinosaur Island and recover Superman.

After Flash and Reverse-Flash defeat Johnny Quick, they force him to confess the Syndicate's true intentions. Lois Lane, who has been investigating the Syndicate since the beginning, films everything, allowing the alliance to expose the Syndicate for who they really are. Upon defeating and sending the Syndicate back to Earth-Three, the alliance focus on finding the last piece of the Equation. Batman soon discovers it to have been inside a Mother Box that Harley kept with her all along, until the Rookie inadvertently absorbed it while sending the Crime Syndicate back to their Earth. Learning that Darkseid is sending his forces to Earth to track it down, the alliance attempts to protect the Rookie. Despite their efforts, Darkseid's general, Steppenwolf, captures the Rookie and takes them to Apokolips. Reunited with Luthor, the League and the Legion invade the planet. Successfully rescuing the Rookie, the alliance defeats Darkseid, whom the Rookie, in actuality an Earth-3 villain, then turns good using the Anti-Life Equation, along with his generals. The alliance then returns Apokolips back to its original place, despite Luthor attempting to abandon everyone again. Upon returning to Earth, the Rookie is given the choice of joining the League as a superhero, or continue working for the Legion as a supervillain, whereupon they leave with their respective decision.

In a post-credits scene, a new enemy arrives on Apokolips and, disgusted by Darkseid's kindness, assaults him.