InGen have decided to shut down the entire Jurassic Park operation, with very secure government permission, so when they go to give the shots with all the animals, there is a struggle, but most of the dinosaurs are killed on day one. Only one protoceratops sneaks into the boat, which nobody was currently occuping, so he was completely unseen. During the voyage back to the San Diego InGen lab, a scientist, Micheal King, discovers the animal and decides to studie it with his equipment. The team reaches the labratory, and Micheal hides the dinosaur in a crate, and manages to get into his office, when John Hammond is already there and discovers the dinosaur, he tells King that it must go to the only one of the two islands that still have dinosaurs(which is Isla Nublar), but King says that he must study the animal speciman more, and Hammond gives him a month. Micheal discovers a Velociraptor embryo in the storage unit, but King accidently drops it, and the dinosaur swallows it, but nothing extraordinary happens. At the end of the month, the Protoceratops lays four eggs, but Micheal does not let Hammond see them. The dinosaur is taken back to Isla Nublar, with a terrible disease most likely gotten from a worker. The eggs hatch two months later, with only one protoceratops, but two velociraptors, and one mixture of a velociraptor head and body, but protoceratops legs, feet, and tail. The protoceratops is discovered by Hammond, but the others get away, making the InGen workers check everywhere in a haste, and find the two protoceratops, one velociraptor, and the mutated one. Micheal, Hammond, two scientists and three workers leave in a cargo ship to take the four back, without anyone realizing that one is missing. The dinosaurs are all set free, but the ship is attacked by five velociraptors, who hide in the back, which Micheal and the scientist Dr. Steven Potter seal shut, but accidently trapping a worker in with the raptors. The raptor's attack lures a tyrannosaurus towards the cargo ship, where it nearly capsises it, but evantually lays in the cargo hold, and Micheal traps it in an attempt to save the crew. The InGen workers try to devise a plan to get the raptors out without dying so that they can open up the cargo hold, let the rex out and find a way out. Just then, a spinosaurus lumbers out, attacks the crew, and kills another worker who was luring it to the forest. Micheal shoots the animal in the heart and kills it before it can hurt anyone else. Meanwhile, the alpha raptor has accidentlly sent the boat towards the mainland with InGen's technology. Micheal decides to shoot the raptors, but Steven Potter says that the glass will break and the entire crew will die, so he decides to devise a plan to kill them on the deck. The remaining crew has the last mercenarie/worker open the back's door, then run to the deck, but the raptors get to him first. The raptors slowly check for any humans, then Micheal, Hammond, and Potter shoot at them, killing one. The alpha and a companion stay out and chase the three into the lower deck and main control panel, but the humans seal it shut, locking the raptors out. They try to turn the boat back to the island, but the raptors seemed to make it malfunction, so the boat is headed strait for the mainland. The alpha and companion break in, but the two scientists, Dr. Sandra Gerry and Dr. Max August, rush in and kill the companion, but the alpha goes on into the cargo, where the humans lock him up with the tyrannosaurus. Hammond says that the two dinosaurs will kill each other, so the crew go onto the main deck, where the two raptors have hidden in the minor control systems, and attack the people, injuring Potter, but they are both shot to death. Hammond and Micheal find out how to turn the ship around, but it is too late, and the ship nearly crashes into the coast of California, but the cargo hold is not opened or harmed. The scientists and Hammond run off the ship, and tell the police about the dinosaurs in the cargo, but when the San Diego's forces arrive, the cargo is opened with both animals gone. The rex is found a week later roaming in upper California, and the forces attack it, but the rex destroys one of the three helicopters attacking, killling 4 officers. Micheal, Hammond, Potter, August, and Max rush out of their helicopter, attacking the beast, but it struggles against them and kills Max by piercing him with it's teeth and being thrown at the operating helicopter's blade. Micheal, deeply sadened, shoots the rex with a tranquilizer two times, bringing it down. It is brought back to Isla Nublar, which the government has decided to never allow anyone, under any circumstances, to enter. Hammond predicts that the rex killed the alpha in the cargo, but it is shown that the alpha is actually alive in an oil field in lower California, where it has met the velociraptor from the InGen lab, and raises it. This sets the climax and ending of the movie.

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