On the Day of the Dead in Mexico, Batman and Plastic Man are in the streets above, tracking the Gentleman Ghost. He fires ghostly exploding bullets at them and Batman responds with grenades, forcing him to lose the money bag. Plastic Man insists on grabbing the money where Batman pursues the Ghost to a nearby cemetery. There's a grave for Batman there, and the Gentleman Ghost fires a blast from his cane, knocking the Caped Crusader into the grave. The Gentleman Ghost prepares to dispose of him but a new hero arrives: Fire. The woman avoids the Gentleman Ghost's bullets and Batman subdues the Ghost using Nth metal brass knuckles and handcuffs. Plastic Man arrives and Batman reminds him to drop the money: all of it.
An ocean liner makes its way across the ocean and a young couple toasts each other. Looking into the sun, they see a horde of pterodactyls approaching them, with gorilla riders. The gorillas, led by Grodd, informs them that the age of the ape is at hand. He shoots the young man and transforms him into a primate.
Batman and Plastic Man are flying over the ocean as Plastic Man tries to apologize. Batman notes that he got the law to help him out but Plastic Man isn't impressed. They get an alert signal and head for the ocean liner. Grodd is testing his evolving ray gun on the other passengers but isn't happy with the results. He takes their jewelry and his warriors take the ship under tow. The heroes arrive and Grodd welcomes the challenge. Batman fires net missiles to snag several of the flying warriors but Grodd uses his mental control helmet to take over Batman's mind. Distracted, Batman doesn't notice one of is approaching missiles and Plastic Man manages to snap him out of it just in time. Batman takes evasive maneuvers but the wing of the Batplane is blasted off and the airplane plummets into the ocean. Plastic Man has formed himself into a glider and gets himself and Batman to a nearby island: Dinosaur Island, which exists outside of time.
An allosaurus attacks them and the heroes run for it. Plastic Man gets his foot stuck and bounces back into the dinosaur's mouth only to have it spit him out. Batman heads toward a ravine edge and Batman swings after him and scoops him up. They swing away to the opposite side of the ravine. Plastic Man wonders if Batman is still mad and explains how he was a low-life crook, Eel O'Brien with the Kiteman's gang. Batman took on the gang and Eel tried to grab the money. Batman brought him down as he tried to escape and he fell into a vat of chemicals. As a result, Plastic Man gained his elastic powers. Batman tells him he'll have to live with his choice.
The heroes find Grodd's fortress and his collection of stolen luxury yachts. Plastic Man starts to look for the stolen money but Batman pulls him back and warns that the valley is lined with security sensors and cameras. Plastic Man makes his way past the security devices with Batman right behind. However, an overconfident Plastic Man sets off the last device and dinosaurs and gorillas surround them. Grodd emerges and says he plans to create a utopia of gorillas, and his e-ray gun is almost ready. The heroes take on Grodd's forces and Grodd himself uses his mind control helmet but this time Batman uses a Tibetan meditation technique to block it. Plastic Man is stretched between two pterodactyls while Batman takes on Grodd one-on-one. The villain knocks him out and the pterodactyls lose their grip, dropping Plastic Man into the jungle.
In the jungle, Plastic Man realizes how Batman rescued him from the chemicals, nursed him back to help, and testified against Kiteman. Batman went before the parole board, giving his word he'd take responsible for Plastic Man's rehabilitation. Plastic Man vows to save Batman.
At the fortress, Grodd fastens Batman to a chair and boasts of how they should join forces to eliminate human scum. Batman turns his offer down and uses secret lockpicks to try and free himself. Meanwhile, Plastic Man sneaks into the fortress but is forced to disguise himself as a shovel... who gets picked up and used by the gorillas.
Grodd is explaining how his new species will bring a new age... and finally notices Batman has escaped. Batman takes on Grodd's soldiers while the villain gets his e-ray gun out. Plastic Man gets into the fortress only to find himself in the treasury. He tries to overcome his greed but can't resist taking as much money as he can.
Batman closes with Grodd only to be hit with the e-ray. Plastic Man arrives and finds himself confronting... Bat Ape. The gorillas close in on Plastic Man and Bat Ape... and Bat Ape informs him he has a plan. Grodd activates his giant e-ray projector which will target everyone in the Caribbean and Florida. Bat Ape uses a batarang to knock off Grodd's helmet and the two apes fight it out. When an ape hits him in the stomach, Plastic Man loses one of the gold ingots he swallowed. Realizing what he has to do, Plastic Man turns himself into a human projector, hitting himself in the stomach to knock out the gorillas with ingots and coins. Grodd grabs Bat Ape but Plastic Man gets to the switch just too late. The wave of energy spreads outward. Batman is back to normal and Grodd realizes he's been turned into a human. Batman reveals he reversed the matrix of the weapon when Grodd wasn't looking. Grodd tries to attack but Batman easily knocks him out. Plastic Man hands over every last jewel and asks Batman to count it, but Batman says he trusts him. Plastic Man thinks about it... and puts in one more jewel he held back.
In prison, a human Grodd is vowing revenge... while eating a banana and hanging from the ceiling of his cell.