A new heroine has arrived in Gotham whose identity is a mystery— even to Batman. During patrol, the Dynamic Duo spots her trying to stop one of Penguin's shipments on Gotham's interstate, using a plasma rifle to send the Penguin's truck with its driver off the bridge. Batman and Robin saves the driver from falling to his death. Batman must figure out who Batwoman is and stop familiar enemies, the Penguin and Rupert Thorne, from selling illegal weapons to the fictional nation of Kasnia. The two employ Carlton Duquesne, a gangster, to provide protection.
Batwoman's main focus is on illegal activity by the Penguin, Thorne, and Duquesne. Despite taking the symbol of the Bat as a sign of justice, Batwoman sullies the Bat prefix by taking out criminals with ruthless and dangerous techniques. She seems uninterested in sparing the lives of her adversaries.
Batman, with Robin, sets out to stop the Batwoman from making mistakes as she tries to take out the villains, and as he encounters numerous twists, setbacks, and apparent false leads in determining her true identity. The newest gadget on display is a wind glider used by Batwoman that utilizes some of the most advanced technology ever seen in Gotham City. Bruce Wayne, Batman's alter ego, also becomes involved with a new lady in his life: Kathy Duquesne, the crime boss's daughter.
In addition to Kathy Duquesne, Bruce is introduced to two other women who, as his investigation into the Batwoman's true identity continues, seem to fall well into suspicion: Dr. Roxanne "Rocky" Ballantine, a new employee of Wayne Tech whose technology development is used by the Batwoman against the Penguin; and Detective Bullock's new partner Sonya Alcana, whose knowledge of the weapons being smuggled by the Penguin and Carlton Dunquesne is much greater than the detective should know. With Carlton Duquesne unable to stop Batwoman's raids on the various facilities used to hold the various weapons, the Penguin calls Bane for additional support to ensure that there are no more losses as a result of the Batwoman.
Not long after Bane's arrival in Gotham, it is revealed that there is not one but three Batwomen, all of whom were the women suspected by Batman; Kathy and Sonia met taking art classes at college and Sonia and Rocky were roommates. They had taken turns to remove suspicion on any one of the three, while using Roxanne's technological genius and contempt for the Penguin (who had framed her long-time fiance Kevin), Kathy's money and access to several key aspects of her father's organization (Kathy wants to end her father's criminal career as it led her mother being killed), and Sonia's physical and police skills to ensure that Thorne's operation is thwarted (as the crime lord previously left her family in financial ruins after arsonists who worked for him burned down her parents' shop and were not punished due to the lack of sufficient evidence). Alcana was also saved by Batman nine years prior, the event giving the detective the original inspiration for the costumed identity she now shares with her friends.
In the final confrontation, a ship taking the weapons into international waters for the exchange is destroyed by a bomb planted by Kathy. She and Batman narrowly escape the explosion despite the efforts of Bane, who falls into the Gotham River and vanishes. At the conclusion, the GCPD are left to assume that Sonia is the only Batwoman after she helps rescue Batman from the ship. Sonia resigns from the police due to the potential problems her presence could cause and decides to leave the city. Batman gives Sonia evidence he discovered which helps clear Rocky's fiance. Carlton agrees to testify against Thorne and the Penguin after saving Kathy's life during the ship's destruction. After she reconciles with her father, Kathy drives off with Bruce.
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