Batman and Plastic Man are in Central America during the Day of the Dead. They’re pursuing the Gentleman Ghost, who has stolen a bag full of money. Batman manages to knock the bag out of his hand and the money scatters all over the alleyway. Plastic Man’s eyes light up and he starts to go after the money but Batman angrily ignores him to save it for later. The Gentleman Ghost passes through a wall and Batman goes in pursuit, but Plastic Man gives into his greed and starts collecting the money.
Batman pursues the Gentleman Ghost to a graveyard where there’s a grave with Batman’s name on it. The Ghost blasts him into the grave and moves in for the kill, but the local superhero arrives: Fire. She draws the Ghost’s fire, distracting him long enough for Batman to hit him with Nth metal brass knuckles, which can subdue even a ghost. Plastic Man arrives late and Batman tells him to lose the money he took.
An ocean liner is crossing the Caribbean when a horde of gorillas riding pterodactyls attacks the island. Their leader, Gorilla Grodd, tells them that he plans to usher in the age of the ape. He fires an e-ray gun at a young newlywed husband and transforms him into a primate.
Batman and Plastic Man are returning to Gotham City in the Batplane and Plastic Man tries to apologize without success. When Batman says he stuck his neck out to get Plastic Man out of prison, Plastic Man complains that Batman is nagging him. They’re interrupted when they pick up a SOS from the liner and go to investigate. Grodd has finished testing his e-ray gun but the passenger test subjects have only partially transformed. He orders his gorillas to tow the ocean liner to his villain headquarters and sees Batman arriving. Pleased to battle the one human worthy of challenging him, Grodd orders his soldiers to attack. Batman brings down several of the pterodactyls with net missiles but one misses. Grodd uses his mental amplification helmet to take control of Batman’s mind, immobilizing him as the missile heads back toward them. Plastic Man manages to snap him out of it but it’s too late: the Batplane’s right wing is sheared off and it goes down in a burst of smoke. Believing they’re dead, Grodd orders his gorillas to continue with the stolen liner. He’s unaware that Plastic Man has shaped himself into a hang glider and flown himself and Batman to the island where Grodd has his base.
Batman recognizes the place as Dinosaur Island, where time has stood still. A Tyrannosaur Rex immediately attacks them and they’re forced to run. Plastic Man is chewed up and spit out with any harm, and the dinosaur corners Batman on a ravine. Plastic Man arrives in time to swing him across to safety on the other side. As Batman recons the island and refuses to speak, Plastic Man wonders if he’s still mad at him. Plastic Man blames Batman for being a freak, noting that he was once Eel O’Brian, a criminal working for Kite-Man When the gang broke into a chemical factory, Batman attacked them and the stolen money was spilled. Eel grabbed the money and tried to escape in a kite glider, but Batman brought him down and he landed in a vat of chemicals. Eel was transformed into a freak with an elastic body: Plastic Man. Batman, unimpressed, tells him that he chose to be a criminal and he has no one to blame but himself for his condition.
Batman locates Grodd’s fortress and the two heroes approach it. Plastic Man sees Grodd’s collection of pirated luxury lots and is eager to find the money, but Batman points out all the security devices. Plastic Man easily slips past them but, overconfident, sets off the last one. The gorillas attack on their dinosaur mounts and Grodd emerges to battle Batman personally. While Plastic Man deals with the dinosaurs, Grodd tries to take control of Batman’s mind. This time the Caped Crusader is ready for him and resists using a Tibetan technique. Grodd boasts that his e-ray is almost ready for use and he plans to create a utopia where apes rule supreme instead of corrupt, evil humans. Plastic Man is caught between two pterodactyls and stretched out, while Grodd knocks out Batman. Plastic Man is snapped free and goes shooting off into the jungle. Grodd takes Batman inside and orders his gorillas to find Plastic Man.
As he recovers, Plastic Man realizes all that Batman did for him: rescuing him from the chemical vat, helping him recover, convincing him to testify against Kite-Man, and vouching for him with the parole board. He vows to save Batman in return.
Grodd secures Batman in his fortress and suggests they are similar, as they both hate human scum. The villain suggests an alliance but Batman isn’t interested. He tries to free himself, while Plastic Man sneaks into the fortress but is forced to disguise himself as a shovel to avoid detection. Unfortunately, a gorilla picks him up and starts shoveling dirt.
Grodd is busy monologuing about how his new species will bring about a utopia… and finally realizes that Batman has escaped. Grodd goes for his e-ray while the gorillas chase down Batman. Meanwhile, Plastic Man has finally slipped away and enters, only to find himself in the treasury. He’s unable to resist and swallows as many gold ingots and coins as he can. Tearing himself away, he arrives in the central chamber only to see Grodd hit Batman with the e-ray. Plastic Man is horrified to see Batman transformed into Bat Ape. Plastic Man wonders if Batman had a plan, and Bat Ape speaks, saying that he still does.
Grodd prepares to active his giant e-ray beam, targeting everyone in the Caribbean and transforming them into gorillas. Bat Ape knocks off Grodd’s mental amplification helmet with a batarang and battles Grodd hand-to-hand. The other gorillas close in on him and one hits the overweighted Plastic Man, forcing him to cough up an ingot. Plastic Man comes up with an idea: he punches himself in the stomach and shoots the ingots at the gorillas, knocking them out. Bat Ape and Grodd struggle near the master switch and the villain is momentarily distracted as his gorillas are defeated. Plastic Man lunges for the shut-off switch… just too late. The e-ray beam covers the entire island and spreads out in a concentric wave. However, all of the transformed passengers revert to human, and all of the gorillas turn into humans as well. Batman also reverts to normal, but Grodd has turned into a human along with his soldiers. Batman explains that when Grodd was distracted, he reversed the programming of the beam. Grodd is knocked out with one punch and Plastic Man picks up all the treasure. He offers to let Batman count it but Batman says it isn’t necessary: he trusts Plastic Man. A disappointed Plastic Man reluctantly coughs up one hidden jewel.
A human Grodd goes to prison where he plots his revenge against humanity… while hanging from his ceiling and eating a banana.