The story begins with an attempt to escape from Rafael Santos' clinic in the Colombian jungle by Drs. Alan Grant and Ellie Sattler. They are caught by the two healthy raptors, now fully trained as guard dogs. When Rafael questions why Ellie referred to one of the raptors as 'Betty', she explains that while her and Alan were treating the raptors, they gave them the names Alf, Betty and Celia. Rafael informs Ellie and Alan that he plans to start training Celia in the morning. After Rafael leaves, Alan and Ellie discuss the possibility that another search team will be sent for them, following the one that the raptors killed.
A newly recovered Dr. Ian Malcolm is then shown getting information on the whereabouts of Drs. Grant and Sattler. The soldier Dr. Malcolm is speaking to tells him that there are units searching for them in the Colombian jungle. Malcolm says that he wants to look for them as well, but he is met with protests, until Robert Muldoon enters the room, offering to look after Malcolm during his search. Malcolm is duly shocked at Muldoon's sudden appearance, because he was thought to have been killed during the Isla Nublar Incident by a velociraptor. Muldoon vaguely explains that he knew the raptors' hunting strategies because he had raised them. Then he tells Malcolm to pack his bags, so that they go can rescue Grant and Sattler.
Back in Colombia, Celia's training is not going as well as Rafael had planned. Celia's aim seems to be off due to her neck injury. Rafael makes the decision to leave her behind when he brings the raptors to Puerto Miranda to disrupt the government's new indictments toward him. The day of the indictment, the raptors cause ample mayhem, but Rafael's plan goes wrong when the power lines cause interference with the raptors' shock collars. The raptors are then able to attack him without consequence. Alf and Betty break Celia out of her pen and kill Rafael, but turn a blind eye to Ellie and Alan, possibly as a gesture of thanks for their kind treatment of them during their captivity.
The story continued in Jurassic Park: Raptors Attack III.