Young Erik Kirby (Trevor Morgan) is tandem parasailing with his mom's boyfriend Ben Hildebrand (Mark Harelik) near a lush island west of Costa Rica. The tow boat drives through a mist, and the tow line is jerked several times. Emerging from the mist, the two men operating the boat are gone, so the boat crashes into rocks. The parasailers unhook their line from the boat and try to control their descent to the uninhabited island.
Toddler Charlie (Blake Michael Bryan) is playing with dinosaurs in his backyard sandbox. Paleontologist Dr. Alan Grant (Sam Neill) tries to correct him as to which dinosaurs are predators, so his baby-toting mom (and paleobotanist) Dr. Ellie Sattler (Laura Dern) has to point out that he's a little young for that much information. Her husband, Mark Degler (Taylor Nichols) appears on the scene, and they have dinner together. As Mark checks on the kids, who've nicknamed Alan the Dinosaur Man, Alan reveals his new research findings to Ellie, who was his former dig partner and fellow survivor of the ill-fated visit to Jurassic Park. Alan tells her that his latest findings have revealed that velociraptors, his primary research subject, were much smarter than they'd previously found. When Alan leaves, Ellie tells him to call if he needs anything.
Alan is garnering scant interest in his latest auditorium lecture, speculating on sonic abilities and thus possible communication between raptors, because his lecture audience only wants to ask about his experiences at Jurassic Park or the San Diego Tyrannosaurus incident. In one answer, he states that nothing could induce him to return to the dinosaur islands.
On a desert airfield/junkyard, men-for-hire Cooper (John Diehl) and M.B. Nash (Bruce A. Young) test out a powerful large caliber weapon, while booking agent Mr. Udesky (Michael Jeter) reassures Mr. Kirby by phone that he has hired the best team and that everything will be taken care of.
Returning to the dig site, Alan tells his assistant Billy Brennan (Alessandro Nivola) that their funding is running out. Billy shows him a model he's created of the sounding space in a raptor skull - it produces an eerie noise when he blows through it. They are interrupted by Paul Kirby (William H. Macy), who invites them to dinner. Billy accepts on behalf of a reluctant Alan. At dinner, adventurous Paul and Amanda Kirby (Téa Leoni) ask Alan to be their guide in a flight over Isla Sorna, the "second island" of Jurassic Park, and offer a generous donation to continue funding the dig.
A small plane flies over the water towards Isla Sorna. Billy sorts his camera equipment, explaining to Alan how the camera bag once saved his life in a gliding incident. Alan falls asleep, and wakes to see the plane empty of people, and a talking velociraptor calling his name ... the voice is Billy's, startling Alan out of this nightmare. As they get over land, the Kirbys and the crew start anxiously looking out the windows, while Alan innocently tries to point out the paleontological sights. When he realizes they intend to land, Alan rushes towards the cockpit to stop them, and one of the men knocks him unconscious. When he awakens, they are on the ground, shouting in the brush for someone named "Eric". Alan tells them the shouting is bad, causing more shouting ... and loud growling is heard. Billy thinks it's a tyrannosaurus, but Alan says it's something bigger. As the group rushes to board the plane, they notice Cooper is missing. Shots are fired in the brush. They start the plane and rev down the runway, when a bleeding, injured Cooper suddenly appears in their path, waving and sobbing for them to stop. Pilot Nash knows he cannot stop - and suddenly a huge dinosaur emerges from the trees and devours Cooper, spattering blood on the plane as it tries to avoid a collision. With the fuel lines severed, the plane crashes through the jungle, losing wings and tail before finally stopping up in a tree.
As the group is recovering their nerves, they find the radio is broken and try to use Paul's satellite phone to call for help, but can't get through. Nash securely snaps the phone into a vest pocket. Moments later, the front of the plane is torn away by a tall dinosaur, who grabs Nash, screaming. He falls to the ground, but the dinosaur scoops him up and eats him. As the monster returns his attention to the plane, everyone rushes to the rear, causing the wreck to overbalance and fall to the ground. The dinosaur rolls the fuselage over and over, tumbling the occupants, and finally tears a hole in the side. As it pokes its snout inside, they run away - and encounter a feeding tyrannosaurus rex. Alan orders everyone to hold still - but they all run. The two giant dinosaurs meet, then duel it out as the humans flee again. During the battle, the larger dinosaur snaps the neck of the tyrannosaur. Alan barely escapes the scene alive.
Finally given some breathing room, Alan's punch knocks Paul to the ground. They finally learn about Eric, and how the boy went missing eight weeks previously. Disgusted, Alan plans with Billy to head for the coast and hope for rescue rather than look for the boy, and given the limited chance for survival either way, the group follows along. Back at the crash site, the group salvages things for the hike, and Alan explains the first dinosaur was of the species "spinosaurus", specifically spinosaurus aegypticus, believed to be the largest and most dangerous predatory dinosaur that ever lived. Billy observes Paul fumbling with his backpack, and confronts him about his adventurous claims - finding out he's not wealthy, Kirby confesses that he's just a small businessman who owns a bathroom and tile store in Enid, Oklahoma. Alan quickly deduces that the check the Kirbys gave him is worthless. The group soon finds the parasail, and Eric's lifejacket and video camera, which proves that Eric was still alive when they landed. Alan suggests they keep the parasail for later use, but as they pull it down, Ben's rotting corpse swings down and entangles Amanda. Hysterical, she runs to a nearby stream, and as Paul comforts her she explains she's more concerned for Erik than Ben. They call Alan over ... and he sees dinosaur eggs in several nests along the river. "Raptor", he whispers, and the group quickly moves on. Alan notices Billy's absence and has to come back for him. When he finds Billy, he explains that he'd lagged behind a bit to photograph the raptor nest.
They find the park building complex and go inside, but a shadow of a raptor runs past a window. Billy smashes a candy machine open while Paul fumbles for change, and as they snack they walk into the incubation room. Amanda walks past the tanks, seeing bigger and bigger dinosaur fetuses, until she sees a full grown head - as she gets a closer look, a raptor jumps out from behind the tank. They run into a cage area where the raptor pins Billy and Amanda behind a cage door - but when it sniffs the air upward and begins to climb, they push the door around and trap it. Outside, the raptors scream to each other. Alan leads the humans into the brachiosaur herd. As the herd starts running, the people are occasionally knocked down - Billy drops his old camera bag, but Alan picks it up for him. Udesky runs into a clearing, but a raptor is there waiting for him, and punches a claw in his back, then leaves. Billy, Paul and Amanda climb a tree, but when they spot Udesky and call to him, he moves, so Amanda feels they should rescue him. As she tries to go toward him, she slips and ends up swinging upside down from the tree, with two raptors below jumping up at her. As they pull her back up, Billy realizes the raptors used Udesky to set a trap. Having failed, a raptor breaks Udesky's neck and the raptors run off.
Alan is trapped by raptors and is looking death in the face when suddenly some tear gas canisters are thrown into the area and their smoke confuses & drives the raptors off. A strangely-garbed figure jumps out and leads Alan away, to his hideout - it is Eric, amazingly alive. He has used supplies from the complex, but also his own ingenuity to survive, learning how to cope with the various dinosaurs. He has read Alan's books, and notices that Alan *liked* dinosaurs before he visited Jurassic Park.
Spending time together, Amanda blames herself for thrill-seeking with boyfriend Ben, because Eric would have been safe at home with dependable (and a bit dull) Paul. He tells her it's not her fault.
Erik and Alan emerge from his hideout, and Alan spots a boat down a canyon. Elsewhere, Billy explains to Amanda that they will not search for Alan because the agreed plan is to head for the coast, and Paul supports him by saying it's logical that the big dinosaurs would be in the center of the island, so Eric is probably headed for the coast as well. In the meantime, Eric explains to Alan that he stayed near the compound because that's where people would look for him ... and that the dinos get bigger towards the coast. Suddenly Erik hears a noise - his dad's satellite phone and the jingle from his tile store. He runs recklessly through the jungle, calling for his mother and father. They happen to be within earshot of his cries and also run in his direction, calling. They meet at a tall steel fence, topped with spikes and lined with nylon cording. After happy greetings, he mentions the satellite phone, and they realize who had it last ... the unfortunate Nash. And as they look up, the spinosaurus has entered the area on Alan and Erik's side of the fence. Alan whispers, "Run!" They run along the fence, the dino chases after them, and luckily they find a space they can get through to the other side before it catches them. After snapping at them through the gap, it seemingly stalks off.
As they make for a nearby building, the spinosaur crashes through the fence. The group runs inside the building and slams a large steel door which surprisingly holds off the dinosaur. Billy anxiously asks Alan for his camera bag back. Alan, thinking that Billy has placed too much importance on his bag, opens it and finds two raptor eggs. Billy claims he was going to use the profits to fund their dig back home. Alan is livid, but stops himself before throwing the eggs out the window. He explains that the raptors wouldn't realize they no longer had the eggs, so he keeps them. He harshly tells Billy he's no better than the people who build the park for profit.
As they descend the stairs to the canyon below, they find the curious screened platforms precarious, so they have to go one at a time. Alan and Amanda make it across a bridge, but Eric is halfway across when Alan realises that the deposit on the handrail is bird excrement, and that they are actually in a giant birdcage ... for pteranodons. Eric is picked up by a mama bird and dropped on a cliff perch, evidently as food for some hatchlings. He runs but there is no way down. Billy is determined to save him, and jumps off a bridge using the parasail - Erik grabs on and they continue to descend the canyon. Eric falls and makes it to shore, but Billy's parachute gets hung up on the side of a cliff face, with an angry ptero harassing him. Amanda gets to Eric, but he is concerned for Billy, and has to be pulled away to safety. Amanda and Eric leave through the gate, but it does not latch behind them. Billy manages to unbuckle his harness and fall into the water, but the fliers are quickly after him. Alan and Paul run down, but he yells at them to get away. A group of the pteranodons are quickly after him, and the water around him runs red. A ptero turns a hostile eye on the two men, and they beat a hasty retreat, plunging into the water and swimming out from under the cage wall.
The group boards the boat and poles it away, and eventually Paul gets the motor running. Amanda seems impressed by his competence. Eric gives his sympathies to Alan for Billy, and Alan expresses regret over his last words to Billy. He realizes that Billy was just young, and that there are astronomers (watchers, like paleontologists), and astronauts. "It's the difference between imagining and seeing." As day breaks, the boat glides past a spectacular field of dinosaurs.
It's dark again, and Paul suddenly stops the boat to listen for a noise. It's the satellite phone, once again. As their eyes sweep the shore, they see large mounds of feces - clearly Nash & the phone have passed all the way through the spinosaur. They bring the boat to shore and shove their arms deep into the mounds, pulling out bones and other items until the phone is discovered. Ignoring the time-share caller they take the phone. To their terror, a dinosaur suddenly pokes its nose into the area - only to walk away because they perhaps smell too badly to be eaten.
Later, they are back on the boat and it's raining. Paul explains there will only be enough juice in the battery for one call, and it definitely should not be to the US Embassy. Eric notices activity in the water - Alan says they are bonitos, and wonders what has spooked them. He orders Paul to get the engine running again, and rapidly dials the satellite phone. Unfortunately, little Charlie picks up. Alan tries to get him to take the phone to Ellie, and reminds Charlie that he's the Dinosaur Man. Charlie goes to take the phone to his mom, but she is outside bidding his dad goodbye and he can't open the door. He gets distracted watching Barney on TV, but then remembers the phone again, and goes to find mom.
In the meantime, the engine fails to catch, and as the spinosaurus attacks the boat, the phone is knocked from Alan's hand. They are forced to take shelter in a caged area of the boat, but the spinosaurus persists in his attacks, puncturing the gas tank and tearing things up.
When Ellie gets the phone, there is nobody there, but Charlie tells her it's the Dinosaur Man. Bemused, she does a call back, and the satellite phone starts ringing. A lucky tip of the boat slides the phone to Alan's reach once again, but the spinosaurus has dislodged the cage from the boat and is knocking it into the water. While Ellie is asking if he's on a cell phone because the connection is so terrible, Alan only has time to shout "site B" and "the river" before he goes under and the call is disconnected. Little Charlie holds up his arms and growls at her, saying "Dinosaur Man!" Her face grows horrified and she begins dialing again.
As the spinosaurus tumbles the cage in the water, seeking a way in, Paul is ejected from the cage. He surfaces, then swims toward a nearby shack with a tall crane over the water. He climbs it, and as the dinosaur has found a way to get a claw inside and has a bloody hold on Amanda, he begins shouting and waving to attract its attention. It comes toward the crane, unnerving him as he tries to decide how to cope with the attention, but at least Amanda, Paul and Alan have been able to climb out of the cage. Seeing Paul's plight, Alan dives under water to retrieve the flare gun. When he surfaces, he fires directly at the reptile's head, which doesn't faze it in the slightest ... but when the flare falls on the water, it ignites all of the leaked fuel. Suddenly flames leap up around the dinosaur, and it knocks over the crane before leaving the scene. Amanda and Eric are devastated, as it seems Paul is dead. But he emerges from the water nearby for a tearful reunion.
As their journey continues, they think they hear the ocean. They all start running, but in the center of a clearing they are suddenly surrounded by raptors. Alan says they want the eggs, and orders the group to their knees in response to the raptor challenge. The raptor sniffs Amanda, evidently suspecting her as the egg-napper. Alan gives her the eggs, which she pushes forward, with her eyes on the ground. Alan spies the sounding model in the old bag, and takes it out and blows on it. The first call is wrong, seeming to set the raptors on edge, but he changes it to better effect. However, the raptors hear another noise entirely, so they call to each other, grab the eggs and swiftly depart. The new noise? A helicopter.
The group runs to the shore and sees a man with a megaphone calling for Dr. Grant. The Kirbys run forward waving their arms, saying it's a very bad idea (as Alan did at the beginning). However, the sole figure on the beach is quickly backed up by helicopters, troop landing ships, and a great deal of firepower. As they board a helicopter, they are in for one more shock - a bandaged but alive Billy is on a stretcher inside. As the choppers fly away, they are passed - by pteranodon, flying free.