A police blimp is flying over Gotham City. A blip ghosts across the radar screen, then the pilot sees something that looks like bat wings fly past the cockpit window. The blimp rises above the clouds, but they see nothing. We flash to the skyline of Gotham, and see a shadow of a giant bat creature flying past against the buildings.
The scene changes to outside of the Phoenix Pharmaceuticals. Inside, a guard is patrolling and making a demo tape for a radio personality ad on a micro-cassette recorder. He hears a crash and goes to investigate. At first he sees nothing, but then a shadow of a giant bat passes over him. The guard is attacked by the creature and drops his recorder under the desk. The guard tosses a chair through the window, and then the bat picks him up and tosses him out and into the river below.
The next morning headline reads, "Gotham Police Declare War on Batman" with a byline reading, "Giant Bat Injures Night Watchman." Detective Bullock tosses it down onto Mayor Hill's desk. Commissioner Gordon doesn't agree with the headline, and doesn't like that Bullock fed the story to a reporter, since it lets Batman know they're after him. Bullock asks Hill for permission to form his own tactical squad, but Gordon has already denied it. They argue about it for a bit, and the camera pans back to show District Attorney Harvey Dent flipping his trademark coin. Hill authorizes the strike force, reminding Gordon that Bullock has a reputation for catching his man. Harvey Dent promises to put Batman in jail if Bullock catches him.
Batman reads the newspaper article and believes he's being set up. He finds out there were two other robberies at pharmaceutical company and chemicals were stolen, just like at Phoenix. Last night's robbery was the first where someone was hurt. Alfred calls off Bruce Wayne's date with "Bambi" as Batman takes off to catch the burglar. Batman reaches Phoenix Pharmaceuticals, and grapples over to the roof. As he flies past a window, he surprises two pharmacists who were making out after hours. They call the police as Batman gasses the police guard and crosses the police line into the scene of the crime. Bullock receives the call from Dispatch, and then calls in his special task force to convene on the building.
While the task force scrambles to his location, Batman sprays the room down to search for clues. He locates a set of footprints belonging to last night's guard, and then finds the micro-cassette recorder underneath the desk. He takes pictures of a shattered jar, and examines some sort of hair, but is interrupted by the arrival of the task force. Bullock sends his men into the building just as Gordon arrives. Bullock is sure they'll catch Batman, but Gordon says another pharmaceutical company was robbed across town. Batman gasses the strike force as he escapes through an elevator shaft. At the bottom of the shaft, he's ambushed by another squad. One of the team members follows him into a room, but Batman grabs him to keep him quiet. The rest of the squad is certain Batman's in the room, and the leader tosses a tear gas grenade into the room, where it rolls up against some gas cans. Batman grabs his temporary prisoner and dives through the window and swings away as the grenade causes an explosion. Batman deposits the squad member on the ground to be retrieved by Bullock and Gordon, and then disappears into an alley across the way.
The next way, Bruce Way arrives at Gotham Zoo, and heads into the bat exhibit, calling for Dr. March. When March appears, Bruce explains that he's there about a possible bat problem, since he keeps hearing squeaks from his chimney. The doctor yells at him for wanting to kill the bats like pests, even though Bruce protests that's not what he's doing. His tirade is interrupted by Dr. Francine Langstrom, who stops her Dad from lashing into Bruce. Kirk Langstrom also comes into the room, giving March a chance to vanish into a lab, presumably to analyze the hair sample. Kirk explains that March gets a little carried away sometimes, as he's really protective of the bat study. Bruce plays the recording of the bat noises for the Langstroms, but they don't recognize the sounds as a bat. Kirk takes the tape and promises to analyze it.
Batman has decided to analyze the sound himself, but he can't find a match either. Dr. March calls at that moment, and lets Bruce know that he has brown bats in his chimney, but they'll leave as it gets colder. The sound on the recorder is actually two sounds, starlings and brown bats, and they're probably fighting over a nest in the chimney. That can't be right, especially since Batman has already ruled out brown bats as being the source of the hair, and the sounds weren't recorded near his chimney anyway. According to the computer, the sounds aren't a match for brown bats and starlings. That means Dr. March is lying, and that makes Batman kind of upset.
Back at the zoo, a shadowy figure is burning the tape and the hair. The figure suddenly begins to suffer an attack of some sort, and takes medicine to stop it. Batman arrives as the figure wanders out of the room, and locates a discarded Phoenix Pharmaceuticals vial. Kirk reenters the room, and finds Batman lurking in the shadows. Batman says he's looking for Dr. March, but he's off at a lecture. Kirk then goes off on a tirade about how they had created a new species, something that was neither man nor beast. The beast is now looking for the final chemical to complete the transformation. Kirk then changes into the giant bat and attacks Batman. Just as the giant bat has Batman pinned beneath a desk, Francine comes in; shaming Kirk and making him flee. Batman attaches his grappling hook to Kirk's leg and they both go flying off into the night.
We see the police blimp again. The pilot sees the blip again, but before his copilot can tell him it's just nothing again, they are startled by Batman crashing into the cockpit window. They call Detective Bullock about the sighting. Bullock tries to leave the police station in a chopper, but Gordon stops him from leaving and causing another fiasco like at Phoenix. They both leave in the helicopter to get to the bottom of this mystery. Meanwhile, Kirk flies Batman through a construction site, causing Batman to bounce off the girders. Batman finally gets a footing as Kirk flies over a girder and yanks the giant bat to him. They grapple and fall towards the ground. Bullock and Gordon arrive and see the giant bat with Batman in tow. Batman covers Kirk's eyes, causing him to crash into a sign, knocking him unconscious. The police copter arrives, but Batman picks up Kirk and flees before they can catch them.
Back at the Batcave, Batman analyzes the list of components that Langstrom used to create the giant bat and develops a way to reverse the process. He arrives at the zoo, where Francine is waiting, and reveals that Kirk is back to normal. The chemical is out of his system, but Batman doesn't believe that this mission is truly over.