Initially players devise their looks, name, and style of fighting, but gain access to super-powers for their character to use as they progress in the story, along with unlocking customisation options.

Labs, and Belle Reve; story levels feature other locations such as Gorilla City, Oa, Themyscira, and Nanda Parbat.

[8] Following the capture of a super-powered individual dubbed "The Rookie", Commissioner Gordon oversees their transfer to Stryker's Island in Metropolis.

As the Rookie possesses a previously unseen ability to absorb energy to gain new super-powers, Gordon offers the incarcerated Lex Luthor a reduced prison sentence in exchange for monitoring them and assessing their potential threat.

Before he can agree to the deal, Luthor's bodyguard Mercy Graves arrives to break him and the Rookie out of prison, and the trio escape alongside several other imprisoned villains, though they are pursued by the Justice League.

The combined group of villains are defeated by the sudden arrival of the "Justice Syndicate", a superhero team from a parallel universe, with only a few escaping.

The Syndicate claim that the Justice League are on an off-world mission and that they are their replacements, with the group's leader Ultraman posing as reporter Kent Clarkson to feed further false information to the public.

Furious at Luthor's betrayal, the Rookie tries to stop him by blasting the machine with energy, causing it to malfunction; inadvertently bringing Apokolips near Earth and teleporting everyone present to random locations.

Batman soon discovers it to have been inside a Mother Box that Harley stole from Wayne Tech, until the Rookie inadvertently absorbed it while sending the Crime Syndicate back to Earth-3.

The Rookie is then given the chance to join the Justice League as a superhero, or to continue working for the Legion of Doom as a supervillain; the choice made is left up to the player.

In a post-credits scene, the angry Anti-Monitor arrives on Apokolips to find all its occupants still under the effect of the Rookie's powers, and proceeds to attack Darkseid, having been disgusted by his kindness.