At the turn of the millennium, Brainiac revealed that he had placed a sleeper computer virus in LexCorp's Y2K bug safeguards which was intended to dramatically boost his abilities. Instead, it allowed his upgraded future self, Brainiac 13, to travel from the 64th century to the present day and take control of Brainiac 2.5's body. Brainiac 13 began transforming Metropolis into the 64th century version of the city, which he controlled. Although Brainiac 13 was able to gain control of several android superheroes, such as the Red Tornado, Hourman, and the Metal Men, and use them against Superman, Superman discovered during a fight with the Eradicator that Brainiac couldn't cope with Kryptonian technology, giving Superman a plan to stop Brainiac's scheme.
With Luthor using a Kryptonian warsuit and aided by Brainiac's past self (now possessing the body of Luthor's infant daughter Lena Luthor), Superman tricked Luthor into plugging himself into one of Brainiac 13's power conduits, claiming that Luthor would channel the energy through a Kryptonian matrix to destroy Brainiac 13. Aided by the revived Red Tornado, Superman managed to suck up the microscopic nanobots that composed Brainiac 13 and transfer them into the warsuit, leaving Brainiac 13 trapped in technology he couldn't understand or use. However, realizing his defeat was inevitable, Brainiac 13 seized his last chance for escape and gave control of Metropolis to Luthor in exchange for Lena/Brainiac 2.5, whom he forced to help him escape.
He returned to Earth along with a teenage Lena/Brainiac 2.5 (or "Leniac"), during the multi-front war against Imperiex. Brainiac 13 claimed to be allying himself with Earth, but this proved to be part of a complex plan to regain control. Remaining behind the scenes for most of the conflict, at the moment when Imperiex's armor was cracked thanks to the sacrifices of Strange Visitor and General Rock, Brainiac 13 appeared on the battleground with Warworld, absorbing Imperiex's energies and vowing to use them to rule everything.
In a desperate gambit, Superman dove into the heart of the sun, thus gaining a massive power boost that enhanced his strength significantly. Rapidly realizing that Warworld couldn't be destroyed without releasing Imperiex and triggering another Big Bang, Superman and the Martian Manhunter formed a brief telepathic link to explain their new plan. With Darkseid's powers weakened, he would use Tempest as a magical focus for his abilities, empowered by the faith and strength of the Amazons, focusing the energy through Steel's new 'Entropy Aegis' armor (which was created from a burned-out Imperiex probe), and, with Lex Luthor activating a temporal displacement weapon, Superman would subsequently push Warworld through a temporal Boom Tube, sending both Imperiex's and Brainiac 13's consciousness back 14 billion years to the Big Bang, destroying both villains through a combined effort. With Brainiac 13's death, Brainiac 2.5 was expunged from Lena, who reverted to infancy, although the control discs remained.
Sometime later, Superman traveled into the future and battled Brainiac 12, learning that everything Brainiac 13 had done in the past had been designed to ensure things reached the point where Brainiac 13 would be created. Brainiac 12's defeat before his upgrade apparently reversed the advances Brainiac 13 had made to Metropolis and retroactively erased Brainiac 13 from existence.
- 22 Appearances of Brainiac 13 (New Earth)
- 2 Images featuring Brainiac 13 (New Earth)
- Quotations by or about Brainiac 13 (New Earth)
- Character Gallery: Brainiac 13 (New Earth)
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