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Like Zod himself, his disciples were defeated and imprisoned in the Phantom Zone. However, Nam-Ek and Aethyr escaped Krypton inside the Black Ship (that also contained Brainiac) just before the planet exploded. Afterward, their mission became clear in freeing Zod on Earth; however, this mission would take them years to accomplish, needing to find the Stones of Power to do so. Aethyr and Nam-Ek were alerted to the location of the stones when Genevieve Teague's blood stained one of the stones. Once Nam-Ek and Aethyr arrived on Earth during the second meteor shower, they immediately set out to conquer the planet in Zod's name and remake it as a new Krypton, but were thwarted by Clark Kent (Kal-El of the House of El).
When Zod's disciples failed to complete their mission, Brainiac created an extension of himself that took on the human identity Milton Fine and set out to release Zod. Due to Brainiac's machinations, Clark nearly released Zod from the Phantom Zone, but he closed the portal just before Zod arrived. According to Brainiac, Clark was originally intended to be Zod's Kryptonian vessel, but Jor-El's spirit proved to be too strong in Clark so Brainiac was forced to turn elsewhere.
Brainiac eventually chose Lex Luthor to be Zod's vessel, and altered Lex's body so that he possessed Kryptonian powers. To prevent Zod's return, Jor-El gave Clark a Kryptonian dagger and told him to kill Lex. However, Clark could not bring himself to do this, and instead hurled the dagger at Brainiac, stabbing him in the chest. However, with Brainiac accessing the Fortress of Solitude through the dagger, Zod's spirit was released into Lex's body. When Clark demanded to know where Lex was, Zod replied that Lex was dead, and gave Clark an opportunity to join him in conquering Earth. When Clark refused him, Zod imprisoned him in the Phantom Zone.