It's a dark winter night in Gotham and a couple dockworkers are suddenly assaulted by a giant bat creature that is very interested in the fruit that they are loading. After gorging itself on some choice pieces, it takes off into the skies and returns home.
Dr. Kirk Langstrom awakens in a panic disturbed by his nightmares. His wife, Francine asks him what is wrong but he says it's nothing. However, when he heads for the window he finds the remains of some of the fruit the Man-Bat had eaten along with some rather large claw marks on the carpet.
The dockworkers explain the attack to some rather skeptical police but Batman is listening and knows exactly what they are talking about. He gets onto his batcycle and heads out to confront Dr. Langstrom.
That morning, Francine finds the torn up rug in the garbage and realizes what's going on. She goes to ask her father about Kirk but he claims Kirk won't work with him anymore. Francine confronts Kirk who is working on a formula that he claims is a cure. She tells him that she can't go through it again but Kirk tells her that he's not deliberately turning into the Man-Bat. Batman arrives and confronts Kirk as well but Kirk continues to deny that he's taken the formula and blames Batman for failing to properly cure him. Unable to take the stress Francine runs from the room while Batman takes a DNA sample from Kirk to confirm that he's telling the truth. All of this is being watched by Dr. March.
Outside, Batman is attacked by the Man-Bat that is wearing the tattered remains of Francine's clothing. This Man-Bat has a distinctive advantage over Batman and he is forced to flee on the batcycle but even going through the subways isn't enough to evade the creature. Batman eventually manages to snag the Man-Bat with his grapple but it's too strong and the Batcycle is destroyed by a train. Fortunately, he has managed to get a hair sample which is all he needs to runs his tests. Meanwhile, Francine has left Kirk who is desperately making calls to the airport. Batman arrives and tells him that his tests have proven that Kirk was in fact cured and that this is a new Man-Bat. Kirk tries to figure out who it is but Batman tells him not to worry about it and instead focus on getting Francine back.
Batman goes to Dr. March's lab and checks his files. Dr. March catches him and threatens to use a tranquilizer on him. Batman confronts Dr. March who admits that he's the one who made the new bat serum and he still believes that only a bat creature can survive the evolutionary cataclysm. He goes on to explain that he worked through the night to refine the formula to make it even stronger but Francine walked in on him and in his surprise he dropped the formula on the floor. Suddenly, March becomes horrified when he remembers that Francine, blissfully ignorant of his experiments, tried to help him clean up the mess but a shard of glass got caught in her skin and she was injected with the serum. Batman angrily asks Dr. March what it will take for him to end the madness and leaves. Realizing that things have gone too far, Dr. March destroys his files. At the airport, Francine complains to the stewardess that she's not feeling well. Unbeknownst to her, Kirk is on the plane and asks her to come home claiming that it can be proved that he's not the Man-Bat, Francine agrees but she's struck by another attack and runs into the bathroom where she transforms. Unhappy with the confinement, she breaks through the plane door causing the cabin to depressurize. Kirk is sucked out of the cabin and the Woman-Bat dives after him. Batman witnesses this but cannot interfere as a stewardess is also sucked from the plane and he has to save her using the batwing. Once the stewardess is safely aboard the plane, Batman goes after Woman-Bat.
Woman-Bat who is carrying her unconscious husband is unhappy to see batman following her and flies him to the top of the Gotham Bridge Tower where Batman confronts her and shoots her with the antidote but it doesn't work. Woman-Bat attacks him and in the fight Batman is nearly forced from the tower but he manages to climb back on and shoots Woman-Bat with another dosage of the serum. This second injection also seems to be ineffective but at last it takes effect and Francine returns to her normal self. Disoriented she almost falls from the tower but Kirk manages to save her vowing not to let her go.