Dr. Leo Quintum and his P.R.O.J.E.C.T. Team are exploring the Sun when they are sabotaged by a booby-trapped, genetically enhanced Lex Luthor clone. Superman saves the day, but it turns out that his body has been overdosed with solar radiation that not only gives him new powers but now is slowly killing him. Luthor, having orchestrated the death of Superman while under the employment of General Sam Lane, is arrested thanks to Clark Kent's article and sentenced to death.
Deciding to keep his impending death a secret from the public, Superman reveals his secret identity to Lois Lane because he wants to spend his remaining time with her. Though Lois was unable to accept it after years of him keeping the truth of his identity as Clark Kent from her, Superman takes her to the Fortress of Solitude. During this visit, Superman's secretive behavior and indirect exposure to alien chemicals heightens Lois's paranoia to the point of attacking Superman with a kryptonite laser. However, seeing the solar radiation has now made him immune to green kryptonite, Superman is able to calm her down and reveals that his secret was that he has been preparing her birthday present: superpowers for 24 hours.
Now as a Superwoman, she and Superman stop an attack by Subterraneans in Metropolis just as Samson and Atlas arrive. Flirting with Lois, and showing a newspaper that reads "Superman Dead, by Clark Kent", Samson is revealed to be the one who stole jewels from an Ultra-Sphinx that he gave to Lois. Answering the Ultra-Sphinx's unanswerable question to save Lois, Superman then defeats Atlas and Samson in a double arm-wrestling match before spending the rest of the day with Lois as her powers fade. Later, Kent meets Luthor for an exclusive interview at Stryker's Island. However, Superman's energy causes the Parasite to free himself and causes havoc in the prison. Clark stops him while not revealing his secret identity, with Luthor disclosing his respect for Clark as both a journalist and a regular person. He then reveals a tunnel from his cell for Clark to escape with the help of Nasthalthia, his delinquent niece. Though Clark asked, Luthor states that he has no desire to escape as long as Superman dies before he does.
Two months later, after taking the city of Kandor to a new planet to thrive, Superman finds Metropolis has been repaired with Kryptonian architecture, and Earth has been protected by Bar-El and Lilo, Krypton's first astronauts, survivors, and Superman's relatives. But, to his dismay, the two have less altruistic goals and intend to turn Earth into a new Krypton. However, Bar-El and Lilo begin showing signs of illness: the two had passed through the remnants of Krypton and thus were saturated with kryptonite. To save them, Superman places the two within the Phantom Zone at their request until a cure can be found.
After settling his affairs in order, Superman proceeds to finish his last will and testament. By then, having reprogrammed one of Superman's robots to get the formula he used to give Lois super powers, Luthor succeeds in making a super serum for himself and tricks the executioners in having him drink it. Escaping, he meets up with Nasthalthia below one of his lairs to continue his plans. Superman finishes off his final entry in the Fortress of Solitude when he learns of Luthor's secret ally: Solaris, the tyrant star computer, which betrayed Luthor by tampering with Earth's sun and turned it blue. With his robots, Superman engages Solaris in space. All seems lost until Superman's pet Sun-Eater sacrifices itself to weaken the tyrant star, which allows Superman to destroy Solaris. Clark returns to the Daily Planet, very ill, to submit his article until he falls dead. As the staff tries to save him, the super-powered Luthor arrives and attempts to kill Lois when Clark comes to and fights off Luthor with a gravity gun. Though the gun is destroyed and he is powerless against Luthor, Superman actually intended the weapon to warp time for Luthor so that his powers burn out early. As his powers fade, Luthor briefly sees the world as Superman sees it, and weeps as he gains a measure of understanding of the universe and everyone in it before realizing his spare serum was taken by Superman who destroyed it.
With Superman's body starting to turn into pure energy, he and Lois embrace one final time and he proclaims his love for her once and for all. He takes off, flying into the Sun as his solar-radio consciousness begins to overtake his body as he enters the Sun and thus saves the day for the last time. One year later, a memorial service is held for Superman. Only Lois does not attend, believing Superman is not dead and will return after he is done fixing the sun. Quintum visits Luthor in his death row cell. Now enlightened from his ordeal and accepting his impending death, Luthor presents Quintum with the only thing that could redeem him for his actions over the years, a formula to recreate Superman's genetic structure through a healthy human embryo. Inside the sun, Superman, now a solar being, is activating and making machinery within.