Set at the beginning of what the Wizard Shazam refers to as "the second age of the great heroes", following the debuts of the Man of Steel, Batman, and Shazam, but preceding the arrival of Wonder Woman, the Flash, and Green Lantern, the story begins with Superman pursuing a group of criminals who have just robbed a museum in Metropolis and used magic against him. Upon arriving in Fawcett City, he finds Shazam already engaged in combat with the same group of thieves. Together, Superman and Shazam defeat a pair of monsters, with Superman impressed by Shazam's ability to repel magic attacks that affect him. Shazam, in turn, expresses envy for Superman's additional vision and breath-based powers. Following the battle, they take a break at Mount Everest, discussing their powers and professional lives as superheroes. Superman steers the conversation away from personal matters, emphasizing his preference to keep his two lives separate. Shazam acknowledges the sentiment but finds it disagreeable. Subsequently, they join forces to thwart the villains Lord Sabbac (whom the museum-robbing gang sought to summon) and Eclipso. In the end, Superman appreciates having an ally in Shazam, better equipped to handle supernatural adversaries.

In a separate subplot, Shazam's nemesis, Dr. Thaddeus Sivana, contacts his business rival Lex Luthor for assistance in defeating Shazam. In return for Sivana selling Luthor back shares of LexCorp he had secretly acquired, Luthor provides Sivana with Spec, a metahuman tracker-for-hire. Spec eventually discovers that Shazam is the alter ego of 11-year-old Billy Batson. Learning this, Sivana sends armed hit men to the subway where Billy lives, with orders to kill him. Using the power of SHAZAM, Shazam defeats his assailants, but in the crossfire, Billy's best friend, Scott Okum, is fatally wounded. Shazam rushes Scott to the hospital, but they are unable to save him.

Unable to extract information from one of the killers, a hired gun with no discernible identity, Fawcett City police, Shazam intervenes, assaulting the suspect to force a confession. The killer reveals Doctor Sivana as the mastermind. Driven by vengeance, Shazam confronts Sivana at his office, causing destruction but stopping short of killing him, despite anticipating further attacks.

Back in Metropolis, Clark Kent, after publishing an article on the Superman-Shazam encounter, learns of Shazam's actions in Fawcett City. He confronts Shazam at Mount Everest, demanding an explanation. Shazam tearfully reveals his motivations, citing Scott as his best friend. Superman, dubious and accusatory, insists on an immediate explanation. Shazam discloses his true identity, transforming back into Billy Batson using the power of SHAZAM, and asserts that being "Billy" might be too dangerous. Superman demands to know who hurt him.

Superman criticizes Shazam for bestowing immense power and responsibility on an 11-year-old, asserting that boys his age should be concerned with "homework assignments and schoolyard crushes" rather than the threat of assassination. He argues that such destinies should be chosen by adults, emphasizing that Billy "is just a little boy!" The Wizard sadly notes that Billy is indeed a child in need of guidance. Superman's demeanor softens, reflecting the gravity of the situation.

The scene shifts to Billy's new home, an abandoned apartment building, where Superman, as Clark Kent, pays a visit. Billy initially mistakes Kent for a representative of social services, but Kent reveals himself as Superman. Seated next to Billy, Kent discloses, "My real name is Clark", suggesting that Superman is willing to mentor Shazam.

The book received positive reviews. The Common Voice suggested that while "Superman/Shazam: First Thunder" may not become a graphic novel classic, fans will enjoy witnessing the collaboration between these legendary characters.^[2] Phillip Hayes of Paperback Reader gave the book an A−, describing it as one of the best Captain Marvel stories.^[3] Newsarama praised Winick for effectively highlighting the differences between the two heroes and commended Middleton's art for enhancing the story's impact.^[4]

The series loosely inspired the 2010 film Superman/Shazam!: The Return of Black Adam.

The series was compiled into a trade paperback: Superman/Shazam: First Thunder (128 pages, DC Comics, May 2006, ISBN 1-4012-0923-8, Titan Books, August 2006, ISBN 1-84576-296-7)

• Superman/Shazam: First Thunder at the Comic Book DB (archived from the original)