The villainous Magpie has broken into an electronic warehouse and is using a headpiece to drain the mind of a psychiatrist, Joe Braxton. Once she's done, she picks up a wooden plaque belonging to the Miskatonic Psychiatric Hospital. As she runs out of the warehouse, Batman attacks her. They spare briefly and he points out that he's been chasing her since she's been robbing electronic warehouses throughout Gotham. Magpie sees Batman's utility belt and describing it as "shiny," asks if she can have it. When Batman refuses, Magpie attacks him with her razor-sharp talons. Batman manages to get a handcuff on one wrist but she knocks him back and escapes into the night. When Batman realizes that he's lost her, he goes to Braxton, who says that he has no idea who he is.
The next day, Lt. James Gordon is having breakfast with his daughter Barbara. Barbara wants to help with his case files, hoping that her father will introduce her to Batman. Gordon reminds her that Batman is a vigilante, not a hero, and breaks the law. Once breakfast is over, he goes out on his job and gets a report about the warehouse assault. Looking over the area, he finds a shelf with disturbed dust and discovers that it has a box of files on prisoners from Blackgate Prison. One of them is for a prisoner named Lunkhead. Gordon is intrigued to discover that Batman left one of his batarangs behind.
Alfred is having breakfast with Tatsu, who is reading the newspaper stories about Batman. She says that the vigilante is a lunatic, and says that she'll stay until Alfred's ankle heals because of her debt to him. Alfred advises her not to make any hasty decisions about staying and going, just as Bruce comes in. He asks Tatsu about how she has been doing since she left the military, and then points out all the subtle body language she has demonstrated that indicate she knew Alfred as a child. Tatsu tells him that her father was partners with Alfred… and then died.
Later, Bruce and Alfred go to the Batcave and Bruce wonders why Alfred never told him about his partner. Alfred says that Tatsu's father died in a car accident and he didn't consider it important. Bruce has doubts about Tatsu and Alfred suggests that he should start testing her. Once he has donned his Batman guise, the vigilante checks the computer records and determines that Braxton worked at Blackgate Prison as a scientist. Another member of his team was Dr. Bethany Ravencroft, who has a practice in Gotham.
That night, Batman goes to the window of Bethany's skyscraper office. He notices her inside but is distracted by two graffiti artists below. He disposes of them and turns back, only to discover that Bethany is gone. Magpie holds up the handcuff from the previous evening and attack Batman, stunning him. She suggests that they could become good friend and moves to kiss him, but Batman says that it isn't going to happen. Furious, she renews her attacks and kicks him over the roof. He manages to catch himself on the way down and returns to the pursuit. When he catches up to Magpie, atman demands to know what she took from Braxton's mind. Magpie says that she'll tell him if he captures her and starts running. Batman manages to snare her leg with a line, leaving her hanging from a ledge. Magpie yells that she won't be caged again and cuts herself free, falling over a dozen stories to her apparent death. However, she heals in a matter of seconds and runs off before Batman can get down. Picking up on her mention of being cages, batman calls Alfred and him check Blackgate records against women matching Magpie's age and general description.
The next day, Gordon tracks down Lunkhead at his day job and tries to talk to him. Lunkhead figures that Gordon wants to arrest him and attack the lieutenant rather than go back to prison. While he avoids thrown crates, Gordon gets a call from Barbara and tells her that he'll have to get back to her later. Gordon then offers Lunkhead candy in return for information about what happened to him at Blackgate. The former villain says that they performed mind control experiment on him to fix his brain, and has no idea why Batman would be interested in what happened. Lunkhead confirms that there was a woman in a cage next to him who was nice to him, but "they" took her away.
As Bruce goes to see Bethany Ravencroft with Tatsu driving him, he calls Alfred. Alfred has identified the female prisoner as Margaret Sorrow, a kleptomaniac and convicted thief. She was sentenced to ten years but was released five years ago after a two-year service, for reasons unknown. Since then, Margaret hasn't been seen. Bruce has Tatsu let him out at Bethany's office and tells her to get a coffee. Irritated at his dismissive tone, Tatsu goes off to punch something.
Bethany's secretary Cassie greets Bruce and leads her into Bethany's office. As they talk, Bruce discusses the Rorschach patterns that Bethany has mounted on his wall, and sees his parents' bodies in one of them. he then gives Alfred a pre-arranged signal to call Bethany, posing as an IRS agent. When Bethany leaves to take the call, Batman searches her office and finds several stolen items. One of them is Braxton's watch, and another is the Miskatonic plaque.
That night, Batman goes to Miskatonic and notices that the lights are on in one room. When he goes in, Magpie attacks him and he slams her back. Unimpressed, Magpie gets up and explains that the scientists took away her ability to feel pain along with the rest of her life. Batman offers to help her get them back, but Magpie slashes him and explains that her claws are tipped with curare as Batman passes out.
When Batman wakes up, he discovers that he's strapped to a lab table with the headpiece on his head. He repeats his offer to help her, but Magpie angrily kicks him. The villainess explains that Braxton created the helmet to remove memories, "rebooting" the subject's brain. However, she plans to reverse the process and put memories back in: her own. A woman screams elsewhere in the hospital and Magpie tells Batman that she has to go recover her memories. She activates the headpiece and leaves, but Batman manages to use a hidden lockpick to free himself from the manacles. Disgusted, he throws off the helmet and smashes it, and then finds the prison file Magpie stole from the warehouse. One of them refers to Margaret Sorrow.
Searching the hospital, Batman finds Magpie, torturing... Bethany. He throws a batarang knocking off Magpie's mask and revealing that she's Cassie the secretary. Batman realizes that Magpie/Margaret/Cassie suffers from multiple personality disorder and that none of her selves know of the others. He tells Magpie that Braxton and Bethany were conducting experiments to reform her, and they succeeded for a while. Magpie receives an early release for volunteering and was given a new life, but she soon reverted to her old ways. Furious, Magpie denies everything and says that she wants Bethany to give her the memories back.
As Magpie prepares to attack Batman, Gordon arrives and shoots off her claws. He then orders Magpie and Batman to surrender. Magpie throws her severed claws at him, taking him in the shoulder, and runs out the door. Gordon orders Batman to stop but the vigilante says that he'll capture Magpie while the wounded Gordon helps Bethany. Gordon reluctantly agrees after Batman points out that they both want to stop Magpie.
Magpie returns to the main lab and finds the smashed helmet. Batman arrives and tells her that they can find another way, but she insists that Margaret is gone and that Magpie is the only one left. She attacks him and Batman manages to take her down by knocking her into a control panel, electrocuting her. Gordon comes in, gun drawn, and Batman tells him that Magpie was driven to get revenge on her tormentors, who she subconsciously remembered. The lieutenant says that Magpie will be sent to Blackgate and Batman points out that there's no justice in sending her to the place where she was created. Gordon says that it's the law, not justice, and Batman wonders what kind of justice he'll get. The police officer admits that he owes him and tells him to leave... this time. As Gordon warns Batman that things haven't changed between them, he realizes that the vigilante has already slipped away.
The next morning, Tatsu comes to pick up Bruce. She sees him enter his study but when she goes in, he's disappeared without a trace. As she looks around, trying to work out what happened, Bruce watches from the Batcave and decides to start testing her.