Gotham faces a brand-new mystery when Batwoman, Kyra Sedgwick, arrives in the city claiming to fight for justice. She operates with a harsher hand than Batman's code, which forbids taking lives, setting up a tense conflict with Kevin Conroy's Batman as he tries to determine Batwoman's true identity. Meanwhile, the Penguin [David Ogden Stiers] and Rupert Thorne [John Vernon] work to move illegal weapons to the fictional nation of Kasnia, hiring Carlton Duquesne [Kevin Michael Richardson] for protection. The stage is set for a clash between rival criminals and Gotham's moral line.
Batman and his young ally Robin [Eli Marienthal] set out to rein Batwoman in, trying to steer her away from deadly missteps as they navigate a labyrinth of twists, setbacks, and apparent false leads in their search for her true identity. On the personal front, Bruce Wayne, [Kevin Conroy]—Batman’s alter ego—enters a romance with Kathy Duquesne [Kimberly Brooks], the daughter of the crime boss, adding emotional tension to the case.
Two other women complicate the investigation: Dr. Roxanne "Rocky" Ballantine [Kelly Ripa] and Detective Sonia Alcana [Elisa Gabrielli]. Rocky, a tech-minded inventor who has tied herself to the Batwoman project, briefly forms a bond with Tim Drake, Robin's alter ego. Sonia, a sharp-eyed officer, seems to know too much about the smuggling network. Batwoman's gadgetry comes from Rocky, financed by Kathy, and the Batwoman persona is crafted by Sonia as a tribute to Batman, who saved her life nine years earlier. The trio's plots reveal that there isn’t just one Batwoman but three, each connected to Batman's past.
During the escalating raids on the weapon facilities, the truth comes to light: Kathy, Sonia, and Rocky are the three Batwomen who had been suspected by Batman. Kathy's plan reaches its peak when she plants a bomb on a ship carrying the weapons for an international exchange. Bane, called in for backup, unmasks Kathy, and Batman and Batwoman narrowly escape as the vessel detonates. In a turn of loyalty, Carlton Duquesne breaks with Thorne and Penguin to save his daughter, and Bane falls into the Gotham River, ending the immediate threat.
With Thorne, Penguin, and Duquesne arrested, Sonia takes the fall for the Batwoman operation and resigns from the GCPD, choosing to leave Gotham behind. Batman provides Sonia with evidence that helps clear Rocky's fiancé, while Carlton agrees to testify against Thorne and the Penguin in exchange for a lighter sentence. In the end, after reconciling with her father, Kathy drives off with Bruce.