The game starts with Gerry Harding (voiced by Jon Curry), the park's chief veterinarian, who is showing his daughter Jess (voiced by Heather Hudson) around the park. At this time, Dennis Nedry puts his plan into motion to shut down the park and escape with the stolen dinosaur embryos. Later, his two contacts, Miles Chadwick (voiced by Jared Emerson-Johnson) and Nima Cruz (voiced by Nika Futterman), realize he's late to meet them at the boat to take them off the island. They head into the park and find Nedry's body. They manage to find the embryos as well, but are attacked by a pack of Dilophosaurus. Miles is killed, but the attacking dinosaurs flee before they can kill Nima. She retrieves the embryo canister and a handgun from Miles' body, but is then attacked and bitten by an unknown dinosaur, fleeing into the jungle.
Meanwhile, Gerry and Jess make their way to the port and come across Nima, who is now delirious from the bite and needs medical attention. The three of them begin driving back to the Visitor's Center, but are delayed by a juvenile Triceratops blocking the road. They manage to get the dinosaur back into its enclosure, but the alpha female appears and attacks, which also attracts the Tyrannosaurus. The trio barely manage to escape, hiding in a maintenance shed as the dinosaurs fight, and deciding to spend the night inside. The next morning, Dr. Laura Sorkin (voiced by Susan Cash), a park scientist who became trapped in a field research lab due to the storm destroying the access road, sees Gerry, Jess and Nima on a security feed, and sends one of the automated tour vehicles to their location to pick them up. The three reach the Visitor's Center unaware that the surviving cast of the movie have just recently fled the island. Once inside, Gerry hears a radio trying to contact them. Locating it, he speaks with Dr. Sorkin, who helps cure Nima of her ailment. The T. rex attacks once again, forcing the trio to avoid it as best they can, eventually managing to lure it away with the help of the tour vehicle. The three regroup back inside the Visitor's Center, but when mention of a rescue is made, Nima pulls her gun on Gerry and Jess and tells them there won't be a rescue.
Episode 2: The Cavalry
Realizing there are still some people unaccounted for on the island, InGen hires a team of mercenaries to rescue them. The team consists of Billy Yoder (voiced by Jason Marsden), Oscar Morales (voiced by Carlos Carrasco) and Danny "D-Caf" Cafaro (voiced by Ari Ruben) . They head to the Visitor's Center to meet with Bravo team, their backup unit, but when they try to radio, all they hear is gunfire. Arrving at the site, they find the team dead save for one member, Vargas, who has gone crazy and tries to attack them. After they subdue Vargas, Yoder and Oscar notice a strange wound on Vargas' arm, speculating that a poisonous animal bite caused him to hallucinate and kill his own men. As they examine the building's the security recordings hoping to find out what attacked Vargas, they run across footage of Nima marching Gerry and Jess out of the building at gunpoint. The Visitor's Center is once again attacked by dinosaurs, which kill Vargas as Oscar and Yoder rush back to the chopper. Meanwhile, Nima, Gerry and Jess are hiking through the woods when they stop to take a break. Gerry convinces Nima to let him start a fire by claiming the smoke will keep any wandering dinosaurs away, secretly hoping the rescue team will be able to see it. Later, while Gerry distracts Nima with questions about her family, Jess manages to steal the radio, slip away and contact Yoder, but is found out by Nima, who forces them to keep moving.
Yoder's team see the smoke from Gerry's fire, but a Pteranodon attacks their helicopter, forcing them to make an emergency landing. While D-Caf tries to repair the chopper, Yoder and Oscar head into the jungle to locate their targets. The pair split up to try and pick up a trail, but Yoder disturbs a nest of Dilophosaur eggs in the process, causing the mother to attack. He manages to hold the creature off long enough for Oscar to arrive and drive it away. At the same time, Nima's group reaches a dead end at the Bone Shaker, an unfinished roller coaster built into the side of a cliff. The trio manages to get the ride operational and attempts to ride it down to the base of the cliff, but as they do so, a pack of Herrerasaurus attacks them. They manage to ward them off, but the coaster cars nearly run off the damaged tracks in the process. Yoder and Oscar locate them and disarm Nima, though she implies that she's met Oscar before. The group heads back to the helicopter, but find that D-Caf has disappeared. The T. rex reappears and makes its way towards them, forcing Oscar to fix the chopper himself. They manage to get into the air just in time.
The last target to be rescued is Dr. Sorkin, and they head out to the field lab to pick her up. En route, Nima gets into an argument with Oscar, clearly having history with him, but the fight is stopped once the group reaches the lab and meets with Dr. Sorkin. However, she refuses to leave with them, forcing Yoder to convince her by exploiting her desire for Isla Nublar to become a wildlife preserve for the dinosaurs. She finally concedes, but asks to be allowed to put an experimental cure for the dinosaurs' engineered lysine deficiency into the water supply to keep the group of Parasaurolophus she has been studying from dying off while she's away. As she, Gerry and Jess do this, Nima tries to hijack the helicopter and escape. Yoder and Oscar stop her, but in the scuffle, a thrown knife damages the controls. Meanwhile, Sorkin's group is attacked by a pack of Velociraptors, forcing them to take refuge atop the water tower. They spot the helicopter and call for help, only for the chopper to crash into the tower.
Episode 3: The Depths
Dr. Sorkin's group manage to escape the falling water tower, fleeing into the maintenance tunnels to escape the raptors. Nima, Yoder and Oscar survive the chopper crash, but all of the mercenaries' weapons are destroyed when the wreckage catches fire. Oscar takes off to scout the area, leaving Yoder to guard the unconscious Nima. When Oscar reaches the field lab, he sees the raptors managing to open to the door to the tunnels, and he follows them inside. Meanwhile, Yoder finds the embryo canister in Nima's backpack, and when she finally comes to, she is forced to make a deal with Yoder to split the profits from the embryo delivery. A Parasaur runs towards them, followed by the T. rex, forcing them to hide in the tunnels as well. Realizing he dropped the embryos during the chase, Yoder goes back out to get them, even while the T. rex still prowls the area. After retrieving the embryos, he and Nima proceed further into the tunnels, but Nima sees glowing eyes in the dark and refuses to continue on without a better light source than the red emergency lights. As Yoder tries to power up the main lights, Oscar tracks a raptor further down the tunnel. He draws his knife and attacks the dinosaur, miraculously managing to kill it in single combat. Afterwards, Yoder and Nima find him and reveal their plan to sell the stolen embyros. Oscar, while hesitant, agrees to go along with it on the condition that he and Yoder complete their original mission to evacuate the other survivors.
Meanwhile, Dr. Sorkin reveals to Gerry that she actually put her lysine deficiency cure into the park's main water supply instead of just the holding pen's, which will eventually cure all the dinosaurs and eliminate Jurassic Park's lysine contingency entirely. As the two of them argue over the ethical implications of Dr. Sorkin's actions, Jess sneaks away with Sorkin's cigarettes, hoping to have a smoke. A raptor attacks her, forcing her to flee back to Gerry and Sorkin, leading the rest of the raptor pack right to them. They fight the dinosaurs off until the others arrive, with Oscar driving the raptors away by wounding the pack leader with his knife. Soon after, steam jets begin escaping from the nearby valves.
Dr. Sorkin explains that this means that the park's power plant is on the verge of an explosion, and will have to be reset manually before it goes off. Now regrouped, the survivors head to the power plant to reset the main grid. The group work together to get inside the plant, release the built-up steam pressure and reset the system, but in the process trigger a safety protocol that begins sealing the entire plant behind heavy metal blast doors. However, the raptors get in just before the doors can fully close, trapping the survivors inside with the dinosaurs. The group heads to the upper level to escape the raptors, but realize that the door controls on their level are burned out, meaning someone will have to go back down to the lower level and use the panel there. Oscar volunteers, and manages to hold off the raptors long enough to reopen the doors before being killed. The rest of the group runs into the boiler room and seal themselves in.
However, once inside they find the body of a man covered in what look like a nest. Yoder identifies him as D-Caf, alive but brain-dead from the same poison that affected Nima and Vargas, with dinosaur eggs laid in his abdomen. Sorkin reveals that the dinosaurs responsible were Troodon, explaining she had been ordered to destroy them after their poisonous bite had been discovered, but couldn't bring herself to do it, keeping them alive in the quarantine pens for study instead. Angered by Dr. Sorkin's actions, Yoder grabs her and draws his knife, threatening to kill her.
Episode 4: The Survivors
As Gerry manages to convince Yoder to let Dr. Sorkin live, Jess discovers a grate leading back into the maintenance tunnels. As they try to open the grate, the Troodon pack returns to their nest and attacks. Yoder holds them back as the group gets the grate open. They run through the tunnels with the Troodon on their heels, but end up getting separated. Gerry and Nima manage to find a ladder and make their way to the surface, but everyone else remains trapped in the tunnels. Gerry tries to go back for Jess and the others, but Nima convinces him they can take care of themselves. During the small break, the two strike up a conversation, with Nima revealing that Isla Nubar was actually the ancestral home of her tribe before InGen brought it out, forcibly removed the native villagers, and built Jurassic Park. She explains that Oscar was one of the InGen mercenaries who originally evicted her people from the island, and she took the job of stealing the embryos for revenge, as well as the hope that the money would help her provide a better life for her daughter. A passing tour car gets their attention, and they use it to head for the park's marine exhibit, which they conclude is the others' most likely destination.
The two groups reunite at the marine exibit, where Yoder explains that they all need to get off the island soon, as the U.S. Navy intends to bomb the island on InGen's behalf to eliminate the threat of potential escaped dinosaurs. Upon hearing this, Dr. Sorkin abandons the group and takes an elevator down to the underwater aquarium, leaving the others stranded topside. The others manage to unlock the elevator and follow her down, where they overhear her on the phone arguing with InGen over the impending bombing, attempting to use the other survivors as hostages to get it called off. When that doesn't seem to work, she releases the park's captive Tylosaurus into the lagoon, despite Gerry's pleading. The newly freed mosasaur slams into the side of the facility, knocking Dr. Sorkin into the moon pool and devouring her.
Yoder calls his employers and has them delay the bombing, but as the group makes their way back to the elevator he pulls out a grenade he took from D-Caf's body, explaining that with his men dead, he only cares about delivering the embryos, and doesn't want the Hardings slowing him down. He offers to take Nima along, but Nima, disgusted by Yoder's betrayal, refuses. Yoder throws the grenade as he escapes to the surface, which cracks the facility's windows when it goes off, causing water to seep in. As the elevator ascends, however, he realizes that the embryos are gone, stolen by Jess while he wasn't looking.
Gerry and the others manage to seal themselves in the aquarium's control room before the rotunda above floods completely, only to find that the damaged pressure seal on the door is causing the moon pool to slowly flood their room as well. Nima notices that the only way out is through a sea cave in the wall of the lagoon, which she remembers from her childhood, that will take them directly to the surface. Donning scuba gear, the three make their through the water and into the cave, narrowly avoiding the mosasaur in the process.
They eventually reach the surface and head for the docks, where Nima's contacts left a boat waiting after Nedry's failed delivery, but are attacked by Yoder as soon as they arrive. As Nima and Yoder fight, the T. rex arrives, and they all freeze in place to keep the dinosaur from seeing them. Gerry kicks the embryo can to distract the T. rex, but Yoder rushes for it, giving himself away and getting himself eaten. Nima manages to grab the embryos as the three remaining survivors run for the boat. Gerry distracts the T. rex so the others can escape, but the T. rex damages the skywalk Nima and Jess are on. As Jess clings to the railing, the embryos fall to the ground below.
It's here the player is allowed to chose whether Nima goes to save Jess or the embryos. If she goes to save the embryos, Nima is eaten by the T. rex while Gerry and Jess escape the island on a boat, with the former deciding to return to his old job as a regular zoo veterinarian so he can be closer to Jess. He also mentions of taking care of Nima's daughter as well.
If the player decides that Nima should save Jess however, she pulls her up while the embryos are crushed under the T. rex's foot. Gerry, Jess and Nima escape the island together. As they sail off, Nima worries how she will take care of her daughter without the money the embryos would have brought her, but Jess manages to find a large case of money in the boat, presumably the payment she would have received for the embryos, implying that everything will work out in the end.