In the final level of the game it is revealed that Brainiac is the mastermind behind the villain's evil doings trough out the game. After tricking the Justice League into teleporting to his spaceship, believing to be the Watchtower, he steal Lily's globe and uses it to power a machine that allows him to teleport away the Justice League and summon different versions of himself from other universes. He gathers multiple versions of himself from each dimension and intends on fusing into one being and obtaining all the knowledge in the known multiverse.

When Maxwell gives a sister to the Doppelganger he realizes that Brainiac was tricking him and uses a warrior to distract him while Maxwell and Lily attempt to protect Cyborg from Brainiac's psychic powers. When it is discovered that Brainiac's machine can't be used against characters that comes from different universes, Maxwell summons alternative versions of DC heroes defeating him.

In the comics Scribblenauts Unmasked: A Crisis of Imagination, Brainiac hires Lobo to capture Maxwell, wanting to mind-control him and use his powers to stop Anti-Monitor from destroying the multiverse. After fighting Brainiac's robot army they decide to have a karaoke contest, Maxwell being the winner makes Brainiac his partner and he joins the fight against Anti-Monitor under Maxwell's command.