January, 1986: Metropolis is still plagued with kryptonite dust, forcing Superman to wear a protective lead-lined suit. Members of the Green Lantern Corps are busy trying to get rid of the last of the kryptonite, as well as the Kryptonian corpses from Argo City. Small-time criminals attempt to haul away kryptonite themselves, hoping to use it against Superman later, but the National Guard stops them; unfortunately, the National Guard has been infiltrated by men working for Kobra. Ra's al Ghul discusses his plans for Superman and Metropolis with Talia, since Batman is still dealing with problems in Gotham City. [“Superman: Kryptonite City, Chapter 1: Radiation”]
Returning to his apartment, Superman causes his lead suit to take on the appearance of Clark Kent, who is known to be sick at home like many of the residents of Metropolis, since a large amount of kryptonite aggravates human illness. WGBS president Morgan Edge calls him to demand that he return to work as GBS anchorman soon, but Clark knows he cannot fit behind the anchor desk with his lead suit and resigns from his job. Daily Planet editor Perry White calls Clark and tells him he's still welcome to work as a freelancer for the newspaper as soon as he's ready. Perry then gets a call from a Jeff Richardson of Nomed Ventures, who wants his advice on buying the Daily Planet; Richardson is actually working for Ra's al Ghul. [“Superman: Kryptonite City, Chapter 2: Resignation”]
As the U.S. Army loads a large amount of kryptonite on a transporter platform, it disappears en route to its destination at a secure facility. Elsewhere, Kobra is alarmed that his technicians have failed to intercept the transport. Ra's al Ghul is also alarmed for the same reason. On Black Island, Lex Luthor is jubilant after having successfully intercepted the kryptonite cargo for his own uses, and his assistants Wanda and Louto praise him. Luthor plans to upgrade his armor. Superman and Kilowog in Metropolis watch as Firestorm uses his matter-transmutation powers to change kryptonite dust into harmless air. U.S. Army General Tom Hartley transports another load of kryptonite, but its intended destination again doesn't receive it. Both Kobra and Ra's al Ghul have double agents in the U.S. Army, while an invisible camera placed there by Luthor watches. On Black Island, Luthor and his Siamese twin assistants Pluto and Plato try with great difficulty to intercept this transport but realize someone else is pirating their pirated signal. Kobra again fails to intercept the transport. Luthor regains the signal, then loses it again. Meanwhile, Ra's al Ghul successfully receives the kryptonite cargo using his pirated signal and plans to let his adversaries fight it out, then deal with the winner. [“Superman: Kryptonite City, Chapter 3: Interception”]
Kobra, angered by his failing to intercept the transport, discovers that the cargo was transported to Black Island. Lex Luthor, already knowing a second party has been involved in the interceptions, realizes that a third party is also involved. Kobra attacks Black Island and penetrates Luthor's defenses. Kobra attempts to blackmail Luthor into releasing the kryptonite cargo, first killing Wanda and then threatening the island itself, a last remnant of the destroyed planet Lexor. Luthor suddenly transports Kobra and himself into the otherdimensional void called the L-Zone and abandons him there, then returns to Black Island under the guise of Kobra, claiming he defeated Luthor. Combining his and Kobra's forces, the location of the third party is tracked to the Middle East. Traveling to the Middle East, Luthor disguised as Kobra suggests a proposal to Ra's al Ghul. [“Superman: Kryptonite City, Chapter 4: Acquisition”]
Luthor, as Kobra, shows Ra's al Ghul a scale model of Metropolis, which he treats with a chemical solution and then fires a miniature energy cannon at it, transforming the entire city into gold. He explains that the gold represents kryptonite, and that he can turn the entire city into kryptonite to become Superman's tomb. Ra's al Ghul is suspicious about the false Kobra's true identity. In the L-Zone, the real Kobra discovers equipment of Luthor's and meets a bald woman named Angela Blake. Ra's al Ghul agrees to Kobra/Luthor's proposal, while CIA agent Cory Renwald, having infiltrated Kobra's organization, overhears and wonders how he can warn his superiors. Privately, Ra's al Ghul reveals that he has guessed that Kobra's true identity is Luthor. Renwald secretly sends an encrypted message revealing Kobra's and Ra's al Ghul's plans to the CIA. [“Superman: Kryptonite City, Chapter 5: Transmutation”]
General Hartley tells Superman about Kobra/Luthor's plan as related by Renwald, who is Superman's foster brother. In the L-Zone, Kobra sets to work on Luthor's discarded equipment and plans to use Angela Blake against Luthor. Superman visits Prof. Bolden, seeking his help. Years ago, Bolden's experiment with using kryptonite as a power source went wrong and caused all kryptonite on Earth at the time to change into iron. Now Superman wants him to recreate the experiment. When Kobra/Luthor's invasion fleet arrives in Metropolis, Bolden's kryptonite reactor – with assistance by Firestorm the nuclear man – nullifies the transmutation device meant to turn the city into kryptonite. The feedback causes Firestorm to revert into his two other selves, Ronald Raymond and Dr. Martin Stein, whom Bolden knows as a colleague and promises to keep his secret. [“Superman: Kryptonite City, Chapter 6: Circumvention”]
His plan thwarted, Kobra/Luthor plans to destroy Metropolis with a barrage of weapons. Now that Metropolis is free of all kryptonite, Superman abandons his radiation-proof suit and stops Kobra's weapons, assisted by Firestorm and John Stewart, Katma Tui, Kilowog, Arisia, and Salakk of the Green Lantern Corps. Superman breaks into the lead ship looking for Kobra and thanks Renwald for his help. He finds Lex Luthor bound in a locked compartment and claiming he was only working as Kobra's prisoner. Afterward, Renwald offers the Siamese twins Pluto and Plato a chance to live a normal life by giving them cloned limbs and body parts to allow them to separate in an experimental procedure, and they agree to testify against Luthor. [“Superman: Kryptonite City, Chapter 7: Back in Action”]