The pair track Poison Ivy to Metropolis, where they find that Poison Ivy has also taken control of Superman. By using a kryptonite ring that Superman entrusted to him, Batman stalls the Man of Steel while Catwoman lets Lois Lane fall from a skyscraper. Superman comes to his senses and saves Lois, and together the heroes capture Poison Ivy.
Later, in Gotham City, Bruce Wayne and Selina Kyle are attending an opera (Pagliacci) when Harley Quinn tries to rob the theater. In the ensuing struggle, Dr. Elliot is killed, and it appears that the Joker shot him. Batman nearly kills the Joker, but former police commissioner James Gordon dissuades him from doing so. Dick Grayson returns to Gotham City for Elliot's funeral. Batman tells him of his suspicions that some mastermind is behind all his enemies behaving so out of character. Behind the scenes a man with a bandaged face appears at all of the crime sites and seems to be orchestrating the plot. He comes to be referred to as Hush.
After foiling an armored car robbery by The Riddler, Nightwing and Batman discover evidence that Ra's al Ghul is also involved in what Batman has come to think of as a grand plot. Batman seeks out Ra's, who tells him that someone from Batman's past has used one of his Lazarus Pits. Returning to Gotham, Batman finds the current Robin, Tim Drake, has been captured by a former Robin, Jason Todd, who had previously perished in the series Batman: A Death in the Family. While fighting Jason, however, Batman realizes that this is not really his old protégé, but Clayface mimicking the identity of Jason.
Batman then finds a mechanical device planted in his computer which led him to seek his old friend Elliot's help. He has a late-night meeting with Harold, his trusted mechanic who has been missing since No Man's Land. Harold admits that someone had treated his disfigured condition in exchange for planting that device, but he is shot and killed before he can name the mastermind. Thomas Elliot is discovered to be the trigger-man, and the face behind the bandages of the mastermind (it is later implied that Clayface had been mimicking Elliot when he appeared to be killed). Elliot held a grudge against the Wayne family since Batman's father, Dr. Thomas Wayne, had saved the life of Elliot's mother after a motor vehicle accident. Elliot had sabotaged his parents' vehicle in order to gain their inheritance. In the ensuing confrontation, Elliot is shot by Harvey Dent and plummets into the water, with Batman never having found a chance to unmask Hush (it is only assumed it is Thomas Elliot). His body is unable to be recovered.
In an epilogue to his face-off with Elliot, Batman discovers that the true mastermind is The Riddler. The Riddler had used a Lazarus Pit to cure himself of cancer, and during his time in the pit, deduced Batman's identity of Bruce Wayne. Having first approached Thomas Elliot with a cure for his mother's cancer (the Lazarus Pit), The Riddler had instead allied with Elliot against Bruce Wayne. Riddler was also the only villain who Batman did not believe acted in an unusual way during the entire saga; the robbery Batman foiled was fairly typical of Riddler at the time. The Riddler also tells him that he and Elliot referred to the plot at the "Hush" plot. Batman convinces the Riddler not to reveal his true identity to anyone else because a riddle which everyone knows the answer to would be worthless.
Another mystery begins troubling the Dark Knight Detective. Even though the man he fought at the graveyard was revealed to be Clayface, Jason Todd's remains are still missing from his grave. The Riddler even taunts Batman of his greatest failure to save Jason's life, and refuses to tell him where Jason's body is.
In the final scene Batman and Catwoman meet. He continues to mistrust her and cannot be sure that she is not more aware of the plot than she admits. While trying to console him, Catwoman inadvertently tells him to "Hush." which brings his fears to light. Catwoman breaks off the relationship with Batman. Though he states that he does trust her, she seems to feel he is not ready to trust completely.
After the story's success, Lee and Loeb were slated to follow the story up with another 6 issues, but the project failed to materialize. Hush's story was continued by AJ Lieberman in the now discontinued Batman: Gotham Knights title.
Two plot elements from the storyline were later altered in other Batman storylines. In Batman Annual #25, it was revealed that Batman was actually fighting the real Jason Todd in the graveyard, who later switched places with Clayface. Also, following Infinite Crisis, it was revealed that the Riddler had spent a year in a coma and lost all memory of ever knowing that Batman was Bruce Wayne.
Craig Lemon from comicsbulletin.com criticized the plot, arguing that too many people now know of Batman's secret identity, opining that the story was not very gripping, and that Batman was depicted as inept for not being prepared for a situation as someone cutting his batline. Nonetheless, he praised the dialogue, the lack of unnecessary exposition, the pacing and action, and minor aspects like the self-defense mechanism of his batsuit. Regarding the artwork, Lemon stated that it touches all the bases, but complained that "it's gritted teeth on all the men. It's huge breasts on all the women. It's impossible anatomy on everyone", though conceding that some readers enjoyed this type of artwork.