New Krypton

Lex ended up imprisoned for his crimes, but rather than going to jail General Sam Lane had him serve out his sentence working for the secretive Project 7734. While still forced to wear chains, Lex was assigned the job of accessing the knowledge stored within the captured Brainiac,[56] who had recently been defeated by Superman (as seen during the "Brainiac" storyline). Lex successfully accessed Brainiac’s brain and after Metallo and Reactron were taken to Kandor as prisoners of the Kryptonians who had now settled on Earth he used Brainiac to reactivate the Coluan’s ship that was also being held in Kandor. Brainiac’s robots attacked the Kryptonians, providing a distraction as Metallo and Reactron used their Kryptonite hearts to kill their captors and murder Zor-El,[57] who is Superman's uncle and the father of Supergirl (the Man of Steel's cousin who arrived on Earth decades after Krypton's destruction).

After his success with Brainiac, Lex was given the seemingly dead body of Doomsday, who had been defeated by the Kryptonians,[56] to study as it had “potential”.[58]

Lex later manages to use Brainiac's connection to his ship to kill the soldiers assigned to watch him. Brainiac manages to free himself from Lex's control, forcing him onboard the ship, and the two make their escape.[59] The two are later shown to have entered into an alliance, with Brainiac promising Lex the Earth when he is done with it. While reading newspapers to catch up on what happened during his imprisonment, Lex learns of the resurrection of Superboy.[60] Lex quickly returns to Smallville, where it is revealed that his physically and mentally handicapped sister Lena Luthor is still alive, and living with her daughter Lori. In an effort to mockingly prove his abilities to Superboy, Lex agrees to cure his sister's illness. With Superboy's aid, Luthor manages to cure Lena, allowing her to walk and think logically again for a brief moment, before he then quickly reverses the process, leaving Lena completely catatonic, and informs Superboy that so long as Superman is alive, he will never reveal how he did it. Lex escapes with Brainiac, leaving Superboy, Lori and Krypto horrified at his cruelty. Because Lex now sees Superboy as a failed experiment of using the "wrong alien DNA," he and Brainiac create another binary clone with their own genetics for another plan to against the entire House of El.[61]