Continuing where we left off in the first part, a chemical accident mutates Pamela's DNA giving her power over plants and Barbara Gordon becomes Batgirl in order to stop Pam from going to jail. But things quickly change when Pamela becomes the super-villain Poison Ivy, kidnapping the Commissioner and placing Batman under her mind-control.
En route to the hospital, Pamela revives and a giant plant knocks the ambulance over, takes out the guards, and pulls her out of the vehicle. It takes her to a greenhouse and embraces her in a healing plant cocoon.
Batman investigates and finds traces of plant life, while Gordon is chastising his daughter. Gordon receives a report on Pamela's disappearance, while Bruce analyzes the leaf sample. A recovered Pamela awakes to find she is part plant and fully healed, and that she can cause plants to grow and obey her mental commands. Barbara is considering her career as a future crimefighter when the plant in her room comes alive and then Pamela arrives.
Pamela toys with Barbara then announces she plans to launch a new wave of eco-terrorism and is taking the name "Poison Ivy." She departs and Barbara decides to help her friend, but can't call in her father since he'll just arrest Pamela. Barbara uses the Bat Signal to contact Batman and brief him on the situation. Batman takes off without her while Poison Ivy breaks into Chlorogene and uses plants to cover the entire building. Batman confronts her and Barbara, dressed in a batlike costume, jumps in to save him. They both end up captured and Ivy drops them off the building. Batman manages to rescue them both while Ivy escapes, and Batman tries to warn Barbara off and reveals he knows who she is
Poison Ivy goes on a rampage astride a giant plant, confronting Commissioner Gordon and the police. She discovers she has the ability to give off spores that makes the police obey her every command. She takes Gordon prisoner and takes off back to the greenhouse, where she dangles the Commissioner over an acid vat. Barbara returns to her apartment and hears the news about her father. Batman tracks her down but Ivy is ready and attacks. Batman is equipped with wrist-mounted "weed cutters" and goes to work (bringing us back to where part 1 began).
Barbara is back to fighting a mind-controlled Batman long enough for him to shake off the pheromones. Ivy is lowering the Commissioner into the acid and Barbara goes after him but is grabbed by Ivy's plants. Batgirl frees her father with an expert batarang throw and Batman uses explosives to knock the villainess out. Batman frees Barbara but Ivy returns on an even larger plant. Batman tries to freeze her with cyro-capsules while Batgirl deals with Ivy's mini-plants. Ivy deflects the cyro-capsules but Batman dumps her into a pond before getting ensnared. Batgirl grabs one of the cyro-capsules and tosses it into the pond, freezing Ivy once and for all.
Gordon thanks his daughter, who reluctantly accepts the name "Batgirl" rather then "Batwoman." She makes her exit and fortunately Gordon (missing his glasses) doesn't recognize his daughter. Later Batgirl and Batman meet and Batman lets her decide to tell her father. She departs but it's clear she plans to continue her new career as crimefighter.