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Brainiac is the true main antagonist of Scribblenauts Unmasked and is based on the New 52 version of the famous Superman villain - in fact the concept of DC's new "52" style multiverse plays a central role in the plans of this particular version of Brainiac.
Using the Doppelganger as a pawn by feigning friendship Brainiac has many iconic DC villains go forth and cause havoc while Maxwell teams up with the DC heroes to stop them - keeping his presence hidden until the end of the game when the heroes beam into his ship and uncover him as the mastermind.
Not wishing to rule or enslave the world this version of Brainiac sought to unlock the multiverse so he could combine all 52 versions of himself into a single, supreme Brainiac and destroy all of creation in the process.