Brainiac (Lance Henriksen) crash lands back on Earth and hijacks Lex Labs to collect Earth's data and amass the power of its weapons systems. Lois Lane (Dana Delany) and Jimmy Olsen (David Kaufman) are sent to one of Luthor's laboratories after Brainiac arrives on Earth on a meteor, successfully dodging attempts made by Luthor's Lex 9000 satellite to destroy him in an effort to boost his popularity against Superman. Superman (Tim Daly) soon arrives and finds Brainiac downloading data from the computers with information relating to LexCorp weaponry. After a fierce clash, Superman seemingly destroys Brainiac with his ice breath.
Witnessing the incident and seeing how Lex's satellite could be used as a weapon against Superman, Luthor (Powers Boothe) retrieves Brainiac's intact brain chip and uses it to reactivate him. He envisions Brainiac as a tool to defeat Superman, then plans to step in and pose as the hero to conquer other planets, leaving Earth under his control. Brainiac accepts the arrangement and begins to rebuild, using Lex 9000 as his new body.
Meanwhile, Clark Kent (Tim Daly) contemplates revealing his secret identity to Lois. With staff shortages, editor Perry White (George Dzundza) sends Clark and Lois to Metropolis to review a restaurant, hoping for a story that will fill the page. Brainiac returns, injuring Superman and Lois with Kryptonite rays, and it is revealed that Lois has been infected with a metallic-based poison that could prove fatal if untreated.
Feeling guilt and urgency, Superman obtains a sample of Lois's blood from the hospital and heads to the Fortress of Solitude to analyze it, discovering that the only cure is Argonium 44, a substance sourced from the Phantom Zone. Brainiac, not far away, locates Superman in his Antarctic retreat and makes a move to download Krypton data from his computer. In response, Superman triggers a self-destruct sequence and escapes to the Phantom Zone, leaving Brainiac to believe him dead.
Brainiac returns to Metropolis where Luthor awaits to fulfill their agreement. Jimmy investigates Luthor and uncovers that he is collaborating with Brainiac, though Brainiac has also removed a self-destructive fail-safe Luthor had planted should he betray him. Superman seemingly returns through a portal and cures Lois, but stepping outside the hospital proves to be an illusion crafted by the Phantom Zone. He is then chased and attacked by Phantoms before making his escape.
Back in Metropolis, Superman and Brainiac engage in an extended battle, during which Luthor is injured in the crossfire. Mercy Graves discovers Jimmy pursuing evidence against Luthor and brutalizes him. He manages to scramble one of Luthor's robot exoskeletons and knock Mercy unconscious, but his camera is destroyed in the struggle, robbing him of proof. Superman appears to have defeated Brainiac and returns to the hospital to cure Lois, but Brainiac attacks the hospital first, smashing the cure, and Superman ultimately destroys Brainiac by breaking his brain chip.
With the cure destroyed, Lois faces certain death. Superman laments never sharing his true feelings and embraces Lois, his tears carrying Argonium 44 that had healed him earlier and curing her. She initially mistakes him for Clark, but he convinces her otherwise. Later, Superman recovers a piece of Kryptonian technology to begin rebuilding his fortress and vows to quit the Daily Planet to spare his loved ones future risk, should any foe discover his secret identity.
The climax leaves an injured Luthor facing criminal prosecution for Brainiac's attack, while Lois rushes to cover Mister Mxyzptlk's looming appearance in Metropolis. Watching Lois's fearless drive to get the story, Superman reconsiders his decision to quit the Daily Planet and chooses to stay close to her.
