Generations follows Superman and Batman from the beginning of their careers to the far future. Each issue contains two stories each; each story takes places ten years after the previous one.
* 1939: The Vigilantes--Superman and Batman meet for the first time, at the Metropolis World's Fair, where they overcome their initial suspicions of each other to team up and defeat the Ultra-Humanite.
* 1949: Family Matters--Clark Kent is married to Lois Lane, and Bruce Wayne's ward Dick Grayson is leaving for college. Lex Luthor and the Joker kidnap the pregnant Mrs. Kent. Batman and Superman are able to defeat the villains and rescue Lois, but in the process the Kents' unborn baby is exposed to gold kryptonite, which means the child will never develop superpowers. The Kents decide to keep the knowledge of his heritage a secret from the child. Meanwhile, Bruce's wife is revealed to be expecting as well.
* 1959: Strange Days---After defeating Bat-Mite and Mr. Mxyzptlk, Batman and Superman face the problems of age and family. Bruce realizes it may be time to retire and let Dick Grayson take over as Batman; unbeknownst to him Alfred is helping to train young Bruce Wayne Jr. ("BJ") to become the new Robin. The Kents discover their daughter Kara is developing superpowers. In the closing panels, an aged Lex Luthor meets young Joel Kent and tells him the truth about his heritage.
* 1969: Changing Times---Kara Kent now helps her father as Supergirl, while Lois Kent is diagnosed with cancer, and Joel Kent is reported missing in action in Vietnam. Dick Grayson, the new Batman, confronts the Joker's Son, who is revealed to be the aged Joker himself. Grayson is killed by the Joker, but Bruce Wayne Jr. (the new Robin) switches uniforms with the fallen crimefighter so that the Batman legacy can continue.
* 1979: Twilight of the Gods---The story opens shortly before the wedding of Bruce Wayne Jr. and Kara Kent. Lois is still alive, thanks to her physician Dr. Holurt. The wedding is halted by a super-powered Joel Kent, who violently kills his sister Kara. Dr. Holurt is actually a disguised Lex Luthor; he reveals to the world that Clark Kent is Superman, then breaks the neck of Lois Lane Kent. Joel's powers are the result of a serum created by Luthor. The serum is unstable (as Luthor knows), and Joel dies a few minutes later. Superman learns that Joel had fathered a child with a young Vietnamese woman, and ask BJ to raise the boy as his own. Meanwhile, a seventy year old Bruce Wayne, on the trail of Ra's al Ghul, is captured by agents of the criminal mastermind.
* 1989: Crime and Punishment---Bruce Wayne Jr., the third Batman, flies to the Fortress of Solitude to arrest Superman. Superman had been hunting Luthor for the past ten years and finally catches up with him (though not before Luthor engineers the deaths of Jimmy Olsen, Lucy Lane, and Perry White, Jr.). Luthor, after exposing Superman to gold Kryptonite, reveals that he is really the Ultra-Humanite. In 1939 he had his brain transplanted into the body of his assistant Lex Luthor (then known as "Ell") after his rocket crashed while fleeing the 1939 World's Fair. The Ultra-Humanite's plan is to move his brain into Superman's. Superman has no choice but to use lethal force on the Ultra-Humanite to escape. The Ultra-Humanite manages to broadcast the image of Superman killing him over worldwide television. Even though he had acted in self-defense, Superman pleads guilty and requests to be sent into the Phantom Zone.
* 1999: Beginnings and Endings---Batman III is brought to Ra's al Ghul, who is actually Bruce Wayne, Sr. In 1979 Wayne Sr. had challenged Ra's al Ghul to face him in the Lazarus Pit; Wayne survived and discovered that the Pit had rejuvenated him and given him incredibly long life. In the years since, Wayne Sr. turned al Ghul's criminal empire into a force for good. Wayne asks Bruce Jr. to take over the operation while he returns as Batman. Batman frees Superman from the Phantom Zone, and they investigate the Ultra-Humanite's death. Batman deduces that the Ultra-Humanite had perfected the super-serum he used on Joel Kent, and was planning to use it after transplanting his brain into Superman's body, as the serum only works on Kryptonians. The serum restores Superman's powers, and he shares it with his grandson Clark Wayne, aka Knightwing. Superman leaves Earth in the capable hands of Batman and his grandson.
* 2919: 1929---Batman travels through space to Superman's Fortress of Solitude, now an asteroid in a distant galaxy. Due to Superman's Kryptonian heritage and Batman's Lazarus Pit treatment, the two have aged at a very slow rate. As they reminisce, Superman recalls that they had actually met in 1929 when they were teenagers. Clark and Lois Lane were winners of a journalism contest held by Bruce Wayne, owner of the Gotham Gazette. While in Gotham City, Superboy joins forces with Bruce (wearing a prototype "Robin" costume) to defeat a gang of criminals. As the story concludes, the two are joined by Lana Lang who, thanks to magical powers, has also gained a long life and married Superman.