Brainiac is the main antagonist of Scribblenauts Unmasked and a supporting protagonist in the sequel comic, A Crisis of Imagination. Unlike his mainline counterpart, his goal is not to enslave or rule the world but rather to completely eliminate all of creation by creating 52 versions of himself and fusing them.
For most of the game, Brainiac was content to watch from behind the scenes, sending DC villains to wreak havoc around the world. It is not until the final level where the heroes meet him in person and he reveals his plan: to unlock the multiverse and use all 52 versions of himself to create a supreme Brainiac and destroy creation itself. To this end, he manipulates the Doppelganger into believing he's his friend.
However, in the comic taking place after Unmasked, A Crisis of Imagination, Brainiac is discovered to simply wanted to have created the ideal world, the issue being that ideal in his eyes was killing everything that wasn't him. He joins Maxwell and the Justice League and aids them in fighting the Anti-Monitor, a being so evil that even Brainiac is disgusted with him. With his "twelve level intelligence" he is a big help to the heroes. Despite this, the Anti-Monitor kills him, but not before demeaning his intelligence. Eventually he is brought back when Maxwell rewrites the universe and destroys the Anti-Monitor once and for all.