It's a late Gotham night, and Batman is meeting with a South Side mobster in Gotham Park. The mob boss has information regarding a train heist that's supposed to go down that very night, but doesn't know much more than that. Batman suspects that the unknown terrorist leader Red Claw may be behind the train heist, and he races over to relay this information to Commissioner Gordon. Gordon can't find anything in the train schedule about a late night route, leading Batman to the conclusion that it must be a "military train, something the government wouldn't want us to know about."
Sure enough, Red Claw is already on the way towards hijacking the Army train carrying a lethal plague through Gotham City. Her gang boards the train and destroys the coupling between the engine car and the plague car. They quickly incapacitate the two remaining soldiers guarding the plague and then blow open the cargo hold door. Their heist is interrupted by the timely arrival of the Dark Knight.
Batman quickly dispatches Red Claw's goons, but the terrorist leader wastes no time in claiming her prize: the plague canister. Upon meeting Red Claw for the first time, Batman is surprised that the terrorist is a woman, but recovers quickly by announcing that "[he's] an equal-opportunity crime fighter." Red Claw is in no mood to tangle with Batman, and holds up the plague canister. If he tries to attack her, she'll unleash a plague to kill them and everyone in a ten-mile radius.
The next morning, Gordon is trying to calm down an irate Army general, explaining to him that if they had known about the plague shipment, they could have taken better steps to prevent the theft. Batman gives Gordon a call, and discovers that Red Claw has demanded a high ransom of gold bullion, or she'll unleash the plague upon Gotham City. While this is certainly a dire situation, Bruce Wayne's attention has been diverted by his lunch date with Selena Kyle. Selena promises a much more exciting date than the last time, but then notices that Bruce seems very preoccupied. (Thoughts of a terrorist unleashing a plague will do that, I guess.) Bruce dodges her concerns, and notices that Selena seems rather pleased with herself. Selena admits that she may have found a way to get the land away from Multigon after all.
Suddenly, Bruce's car is rammed from behind. Red Claw's thugs have finally tracked down Catwoman and plan on ending her interference with Multigon's plans. As the thug's car passes Bruce, he recognizes one of the men from the train heist and he races onto the bridge and speeds away from the car. He then whips the car around and nearly causes a head-on collision with the thugs. Instead, Red Claw's thug careens off the side of the bridge and into the river below.
Bruce escorts Selena home, and asks her to confide in him if she's in some sort of trouble. Selena tells him she's not very good at "playing the damsel in distress" and heads inside her apartment, where she promptly changes into her Catwoman costume. She knows the thugs who tried to kill her were from Multigon, so it's time to find out what they're really up to. Meanwhile, Alfred is trying to help Bruce determine why Red Claw would want to harm Selena. Bruce hands Alfred his jacket as he begins to change into his Batman costume, and Alfred pulls an unusually-colored hair from the back of the jacket. Batman quickly recognizes it as a cat hair, and immediately realizes where he's seen this particular shade of cat fur before: On Isis, Catwoman's "sidekick."
Later that night, another Red Claw thug breaks into Selena Kyle's apartment, where Maven is relaxing. The thug sneaks up behind her, but Maven catches sight of the thug in the glass surface of the coffee table and throws a glass of lemonade in his face. She tries to escape the apartment, but can't open the door because she's forgotten to remove the privacy chain. Just before the thug can harm her, Batman arrives and beats the thug into unconsciousness. He then turns to confront Maven, and informs her that he knows Selena's true identity. Maven tells him that Selena has gone to the Multigon site to confront Red Claw. She also tells him that Selena has fallen in love with Batman. This information really seems to hurt the Dark Knight, because he knows that a relationship with a cat burglar will never work.
Catwoman makes her way into the underground missile silo and begins snapping pictures of the resort's true nature. Unfortunately, her spying is interrupted by the arrival of two Red Claw goons. Before they can sound an alarm, Batman arrives and dispatches the guards. They begin to rush out of the silo, but are quickly captured by Red Claw. She ties the two together and then places a canister of plague next to them. She informs Batman that she has no intention of unleashing a plague upon Gotham when she can just as easily make Gordon think that she's got the plague. However, she's more than happy to use the plague to get rid of Batman and Catwoman. She places a few drops of acid on the plague canister, and tells her goons to sound the evacuation signal and to seal the compound.
Catwoman slices through the ropes so that they can make their escape. As the doors to the silo begin to close, Batman tells Catwoman to make her escape so he can destroy the plague. He races over to a fuel truck and begins pouring gas throughout the compound, spraying heavily in the room with the plague canister. He then swipes a grenade from a nearby crate, steals the fuel truck, and tosses the grenade out behind him. A fiery explosion quickly engulfs the plague canister and takes out most of the silo. Batman steers the truck toward a cargo helicopter, blows that up, and proceeds to destroy the rest of the facility. Red Claw screams out her defeat from a higher ledge as she watches the facility go up in flames, and suddenly Gotham Police copters soar into the area to round up the rest of her goons.
Red Claw doesn't plan on going quietly, and she races over to where Catwoman is watching the destruction to take out her frustration on the costumed thief. Red Claw nearly knocks Catwoman off the cliff, but her assault is stopped by the timely arrival of a mountain lion. Catwoman gives a last glance to Batman and then makes her escape. Batman lets her go; after all, he knows where she's heading.
When Catwoman arrives home, Batman greets her there. Catwoman asks if he's notified the police about her whereabouts, but Batman says, he "didn't want [her] taken away like a common criminal." Catwoman is happy, thinking that Batman is finally returning the feelings she has for him, but as she approaches for a kiss, Batman snaps handcuffs onto her wrists. He does admit that he cares for her, more than she'll ever know, but justice must be served nonetheless.