The original Braniac had downloaded itself into Doomsday's body in an unsuccessful attempt to beat the Man of Steel; to save itself at the last second Braniac dowloaded itself into a new body, upgrading itself to Braniac 2.5.

Braniac 2.5 decided to take advantage of the new millenium to take over Metropolis. Using Lexcorp's Y2Kompliance software, it caused a worldwide shutdown, the realization of everyone's nightmare about January 1, 2000. Defense systems worldwide went haywire, and the JLA and Superman scrambled to stop all the nuclear missiles which had simultaneously launched.

But something went wrong with 2.5's plan.

Braniac-13, an upgraded version of the Braniac program from the distant future, took advantage of its previous iteration's actions to download itself back through time into the present, erasing all the previous versions in the process. Braniac 2.5 saved itself at the last moment by downloading into the consciousness of Lena Luthor, Lex Luthor's infant daughter.

Braniac-13 set about transforming Metropolis with its own futuristic programming, turning Superman's city into a true City of Tomorrow. Braniac-13, or B13, also set about its task of destroying Superman, using as its unwilling pawns every technically-augmented or robotic hero on the planet, from Red Tornado and the Metal Men to John Henry Iron's Steel armor, as well as the evil Metallo.

Superman and Lex Luthor (being guided by Braniac 2.5's consciousness inside his daughter's body) both realized that Braniac-13 was powerless against Kryptonian technology, and used it to win against B13. While Superman battled B13, Luthor climbed into the Kryptonian warsuit he had stolen form the ruins of Superman's Fortress of Solitude and, with Brainiac 2.5's assistance, shorted out Brainiac-13. The battle seemed over. At the last second, however, Luthor struck a deal with B13, exchanging his daughter for total control of the B13 technology which had transformed the city of Metropolis.

Everyone thought the Brainiac-13 threat was past. But Brainiac-13 was in fact simply biding its time. When Imperiex arrived, intent on destroying Earth and the rest of the universe, Brainiac-13 reappeared, taking a direct hand in the battle and revealing its ultimate goal just as Imperiex Prime prepared his final assault.

Brainiac-13, in control of a new Warworld, activated the Lexcorp towers, which were in truth a giant energy cannon, and fired a shot at Apokolips, home of the evil Darkseid, who had forged an alliance of necessity with Earth against Imperiex. While both worlds reacted to what seemed to be an attack on Apokolips by Earth, Brainiac-13 used Warworld's energies to capture and imprison Imperiex, giving Brainiac-13 access to Imperiex's powers.

Superman flew to Warworld, intent on destroying it. Unfortunately, he soon realized the truth--that if he destroyed Warworld and Brainiac-13, Imperiex would be released, able to continue his mission to destroy the universe.

Superman devised a plan, which he shared with Darkseid and President Luthor. Combining Apokoliptian and B13 technology, they opened a boom tube which allowed Superman to push Warworld, Brainiac-13, and Imperiex through to the beginning of time. There, caught up in the massive energy release of the Big Bang, the threats of both Imperiex and Brainiac-13 were destroyed.

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