Gotham City had suffered the results of a magnitude 7.6 earthquake in the earlier Cataclysm storyline. With hopes for rehabilitating Gotham bleak, it was declared a No Man's Land by the US government, which effectively quarantined the entire island city. Bridges were destroyed, and any other means of entering or leaving was guarded by the U.S. Army. While the JLA did not assist in the quarantine for ethical reasons, they were so occupied keeping outside forces from conquering the city, that the situation inside was left to Batman and his allies.

Inside the city, the freed inmates of Arkham Asylum battled for control, as did various gangs. Fighting to reduce the chaos were the members of Gotham's Police Force who chose to stay behind, as well as heroes like Oracle and Huntress, who adopted the Batgirl persona in Batman's absence. He had left the city as Bruce Wayne, to try to solve the problem politically, using his fame to try to convince the government to free his city. His efforts failed, and about 100 days later, he returned to Gotham and his people, many of whom had long since given up on him. Even his former partner, Jim Gordon, believed that Batman had abandoned Gotham to the Arkham escapees.

What Batman returned to was a system of anarchy on a grand scale. Since there was no longer anywhere to spend it, money became worthless, so people would barter anything from batteries to services to protection for daily necessities. It seemed the only person to have any use for cash was the Penguin, who had nightly soires where those few with cash left spent it all on such rare and simple items as an apple. The Penguin had his own mysterious leak to the outside and apparently enjoyed taking advantage of the dire situation in Gotham.

With Batman being gone for so long, and his very existence debatable in the Gotham underworld, the Huntress was able to pass off as not Batgirl, but Batman himself to many of the criminals she faced. Following the example of the gangs in town, she even tagged by graffitti her territory with the bat symbol. She went back to her Huntress costume when the Dark Knight confronted her, without any pleasantries. The real Batgirl, Cassandra Cain, made important contributions to the effort during this time, as well as starting a lasting friendship with the Oracle.

In an effort to redeem herself, the Huntress went to the aid of a church that was open as a hospital and sanctuary to anyone desiring it in Gotham. Having no protection because of their benevelent intentions, the church and its kind staff were sitting ducks. The Huntress' desires to use her expertise to protect them was seen more as an unnecessary and warlike show of force than as help, even when she was trying to halt the Scarecrow's machinations to sabotage the church's efforts.

It seemed to the Huntress that no matter what she did, she could never get approval from Batman.

A few other members of Batman's Rogue's Gallery were there to help maintain the terror, though even they still had to improvise and live difficultly, as did everyone else. Two-Face caused problems for the police, Poison Ivy took over Robinson Park (though in the series Ivy did not act as a villain; she instead cared for numerous orphans, was nearly killed by Clayface, and in a deal with Batman was left alone in exchange for her providing fresh produce twice a week to the remaining citizens), Zsasz owned his own territory. Despite his status as a supervillain, the Scarecrow was welcomed into a church filled with refugees and manipulated various factions in a plot to send the church's refugees spiralling into fear and despair. The Joker made the most of his rare appearances. Near the end of the saga, he lured Sarah Essen, Commissioner Gordon's wife, into a twisted game of cat and mouse. He ended it by fatally shooting her. In an act of rage, Gordon shot the Joker in the knee.

Much of the storyline was narrated by Oracle, as she used her resources to become a low-tech version of herself. She used paper to document events and the passage of time, operatives and emergency phones (knowing which ones were still in operation) to gather intel, and maps coloured by pencils to keep track of who controlled which portions of the city at a particular time. Her maps were frequently shown in the comics to help the reader follow the progression of territorial disputes (Gotham City maps in current series are based in large part on Oracle's maps from this series). Oracle remained one of the few people in the city with the ability to contact the outside world.

Like Oracle, all of the characters got serious testing of their mettle. Commissoner Gordon became more of a general leading an army than a police officer, and held a grudge against Batman, even after he had returned. It wasn't until nearly the end of the storyline before they talked again, and Batman even revealed to Gordon his secret identity, in a gesture to regain his trust, but Gordon turned away without looking. He didn't want to know who was under the mask, and told Batman to put it back on.

Eventually, thanks in no small part to the machinations of Superman nemesis Lex Luthor, Gotham City was released and rebuilt, and rejoined the United States.