In an undetermined future, the giant city of Metropolis is starkly divided between upper classes who live in luxury and lower classes who toil under harsh conditions. Clarc Kent-son, son of Jon Kent, the Great Architect and apparent Master of Metropolis, becomes aware of the social inequality after meeting Lois, a teacher from the undercity. He joins the workers to experience their daily lives, then begs his father to improve their lot, but in vain. In reality, the city is in thrall to the scientist Lutor, an old colleague of Jon Kent from before the "time of smoke and soot" that came before the foundation of Metropolis. Both Jon and Lutor fell in love with the same woman, Marta. When she chose Jon over Lutor, the scientist killed her, then used advanced hypnosis to turn Jon into his mind-slave. Concerned about a potential revolution, Lutor identifies its leader, Lois, who prophesies about a coming savior who will reunite the city. Later, Lutor captures Lois and uses her to create a robotic duplicate which he names Futura that will lead the workers to their doom. Meanwhile, Clarc discovers that he was a foundling adopted by Jon and Marta after he was found in a capsule that fell from the sky, and that Lutor, who discovered his powers while trying and failing to kill him along with his mother, blanked away his memories and blocked off his powers, turning him into a social drone. As Futura, disguised as Lois, leads the workers to a doomed rebellion, Clarc, now the Super-Man, the savior of Metropolis, intervenes. He fights, and defeats Futura by throwing her into a tank of molten metal. Meanwhile, Lutor reveals his metallic body powered by a kryptonite heart. He kills Jon Kent who, in the end, sacrifices his life for Clarc. Lutor is later destroyed by Clarc after a fierce battle. Clarc and Lois become the new, enlightened rulers of a reunited Metropolis.

Metropolis is at peace. Lois researches the history of the city with the help of Steve Trevor-son. They discover information about the three founders of Metropolis, Jon Kent, Lutor and Paula von Gunther, who crossed the "black sea" after the "time of smoke and soot" to create the city. Trevor-son, meanwhile, is in thrall to the exotic dancer Diana, known as the "Blue Amazon", who appears at Dr. Psykho's Palace of Sin, the last remnant of Lutor's criminal empire. Psykho exploits the amnesiac Diana, who was given to him by Lutor, but cannot divine her origins. When Trevor-son tries to free her, he is taken prisoner. Meanwhile, a creature, the Cheetah, has come to Metropolis looking for Diana. After a brief encounter with the Nosferatu, the Cheetah locates Diana. Psykho uses his mental power to learn the truth. Metropolis is on a terraformed Mars, where the survivors of Mankind, led by Jon Kent, Lutor and Paula Von Gunther, resettled after Earth was wrecked by pollution. Biologist Paula von Gunther later left the others and created her own artificial, flying city, known as "Heaven", where she used her knowledge of genetics and the genes of the Earth animals she saved, to create her own race of beast-like Amazons. Diana is her perfect clone. Later, needing new gene stock, Paula sent Diana to Metropolis below, where she was captured and had her memories erased by Lutor. In Heaven, the Cheetah led a rebellion and killed Paula. But now, she, too, needs Diana in order to save the Amazons. Psykho makes a deal with the Cheetah: he will give her Diana if she kills the Super-Man. The Cheetah leads her Amazons in a battle royale against the Super-Man, who is then assisted by the Nosferatu and the inmates from the Asylum. When Psykho tries to kill Trevor-Son, Diana's love is enough to restore her memories. She becomes the Wonder Woman, challenges the Cheetah to a duel and wins. Peace is restored to Metropolis; the three "worlds", above and below the city, are reunited; the truth about the past has at last been learned.