Catwoman is on the run, and Batgirl is right behind her. It's chase, run, jump through the rooftops and streets of Gotham until, finally, Batgirl commandeers a Taxi and orders the driver to catch Catwoman. Suddenly the Taxi skids out of control! The Taxi Driver vanishes into thin air, along with every single Man and boy in Gotham City!

Gotham City launches an investigation into the mysterious disappearance of the Male Population. But it's a vicious catfight as the acting female Heads of State argue for political power. The female Commissioner appears to have the crime situation under control until Harley and Ivy decide to finish what Catwoman started and break in to the Police Dangerous Evidence Vault.

Batgirl surprises Harley and Ivy as they ransack the Dangerous Evidence Vault. Harley & Ivy serve up explosive surprises from the buffet table of supervillian technology stored, but Batgirl is holding her own against until her efforts are undermined by interference from the overzealous female Commissioner, letting Harley & Ivy escape. The Commissioner blames Batgirl for the escape and declaring her persona-non-grata to all Police Personnel.

Batgirl surprises Catwoman rifling through a computer belonging to a Detective Reesdale ­ a woman who disappeared at the same time as the men. Working together they discover the missing Detective's secret which may help explain the disappearance. But when they find out the device has been stolen by Harley & Ivy during their raid of the police vault, everything is thrown into jeopardy!

Harley and Ivy escape, but Catwoman is arrested and blamed for the three day disappearance of the men of Gotham. Batgirl – as Barbara – tries to convince her father of Catwoman’s innocence, but he is unyielding. Harley and Ivy – trying to help the captured Catwoman - are themselves arrested. Batgirl is alarmed by the ferociousness of the Police and disturbed by her father’s apparent sanctioning of this new brutality.

Batgirl pays a visit to Commissioner Gordon to express her concern over his new “Get Tough On Costumed Villains” policy. She suspects that he is experiencing some kind of post-traumatic shock because of the three days he and the men spent lost in suspended animation. Unable to persuade the Commissioner of the danger Harley, Ivy and Catwoman are in, Batgirl takes the unprecedented move of breaking them out of prison. They are safe, but Batgirl has been declared “Public Enemy Number One.”

Detective Montoya is arguing with Commissioner Gordon when the call comes in that Batgirl has been spotted on the North Side. As they head off, Batgirl is sighted on the West Side. Then the South Side. Each of these “Batgirls” is unmasked, revealing them to be Harley, Ivy and Catwoman. Under cover of this diversion, Barbara Gordon slips into the unmanned Police Headquarters and steals the key to the Dangerous Evidence Vault from her father’s drawer. As she slips the key into the Vault she is surprised by Detective Reesdale.

Detective Reesdale assumes Barbara has the Commissioner’s permission and gives her the "grand tour" of the vault. Reesdale lets slip some information that disturbs her. Barbara secretly steals some of the evidence confiscated from Mr. Freeze and slips away. In the glare of the Bat-Signal, Barbara confronts her father. When he insists he has incontrovertible evidence implicating Batgirl, Barbara’s fears are realized. Her eyes turn to steel. She forces the Commissioner into the Batsignal and to certain death. What’s wrong with this picture?

The Commissioner, twitching in the Batsignal, explodes into a pile of gears and wheels and microchips: He’s a Robot! Who is behind this robotic Commissioner? None other than the Commissioner’s supposedly loyal assistant, Dora Smithy. Sister to Nora. Sister-in-law to Mr. Freeze. The Robotic Replacement was designed to crack down on the costumed villains – like Mr. Freeze – whom Dora blames for her sister’s fate. In a final pitched battle in an old Mr. Freeze hideout, Dora falls into a vat of cryo-solution and is turned into a female version of Mr. Freeze. The very thing she hated.