Brainiac appeared again to battle Superman briefly (Superman: The Doomsday Wars mini-series 1999), and it was believed that he was destroyed in the encounter. The remains of his body were retrieved by a Coluan scientist, Prin Vnok, who transferred Brainiac's consciousness into Doomsday's body, retrieved from the end of time. He defeated the Justice League and took Pete Ross and Lana Lang's newborn son to grow into a more controllable Doomsday body. During a battle with Superman, his mind was ejected from Doomsday, allowing the monster to go on a rampage before being imprisoned by Superman and the JLA. Brainiac transferred his mind into a permanent robotic body (known as Brainiac 2.5), and escaped to an unknown location.
New Year's Eve 2000 saw the return of Brainiac 2.5 who, in an attempt to upgrade his new robotic body, found himself unable to control the download of a future version of himself known as Brainiac 13. Brainiac 2.5 transfered his conciousness into Lena Luthor while Brainiac 13 brought about the complete upgrade of Metropolis to a futuristic hi-tech city. Brainiac 13 was finally trapped by Superman's use of Kryptonian technology, but not before B13 convinced Lex Luthor to sacrifice his daughter as an avenue of escape in return for the "keys" to the new Metropolis (Superman Y2K [4 part storyline]).
Brainiac 13 returned as a surprise villain at the exact time of the defeat of Imperiex. In command of a new War World, Brainiac 13 planned to syphon the world-destroying power of Imperiex for himself (SUP #173). However he was thwarted when Superman, pulled together a plan with Steel, Luthor, Darkseid and others, to push Warworld, B13 and Imperiex through a boom-tube to the beginning of time (ACT #782).
Brainiac later returned to aid Lex Luthor and a brainwashed Superboy in their assault on the Teen Titans and Outsiders through his "granddaughter" Brainiac 8, the secretly reprogrammed Outsider Indigo. His plan, hatched in part to preserve his homeword of Colu from its supposed destruction in the future by Donna Troy, appears to have failed.
First Appearance: AOS #438 (July 1988)
First Appearance (with his Coluan body): ACT #649 (Jan. 1990)
First Appearance (as Brainiac 13): Superman Y2K (March 2000)