A saber-toothed squirrel (known as Scrat) is trying to find a place to store his prized acorn. Eventually, as he tries to stomp it into the ground, he causes a large crack in the ground that extends for miles and miles and sets off a large avalanche. He barely escapes, but finds himself stepped on by a herd of prehistoric animals. The animals are trying to avoid the ice age by migrating south. Sid, a clumsy ground sloth left behind by his family, decides to move on by himself but is attacked by two Brontops whom he angered. Sid is soon saved by Manfred ("Manny"), an agitated mammoth who fights them off and is heading north. Not wanting to be alone and unprotected, Sid follows Manny. Meanwhile, Soto, the leader of a Smilodon pride, wants revenge on a group of humans by eating the chief's baby son, Roshan, alive. Soto leads a raid on the human camp, during which Roshan's mother is separated from the rest and jumps down a waterfall when cornered by Soto's lieutenant, Diego. For his failure, Diego is sent to find and retrieve the baby.
Following a nuclear test in French Polynesia, the fallout irradiates a lizard's nest. Decades later, an enormous sea creature suddenly attacks a Japanese fishing vessel in the South Pacific, leaving only one fisherman alive. Dr. Niko "Nick" Tatopoulos, an NRC biologist, is sent to Tahiti and to Jamaica, where a wrecked village, footprints, and ship are found. Nick collects skin samples that lead him to believe the creature is an enormous mutant created by nuclear testing. It travels to New York City during the rainiest week of the season, leaving a path of destruction in its wake.
Tourists Ben Hildebrand and Eric Kirby decide to parasail around the island of Isla Sorna. A creature of unknown species attacks and kills the boat crew as it passes through a fog bank, but Ben uncouples the line, and with Eric bound with him, he goes sailing into the wilderness.
It has been four years since the events of the first movie. Seventeen-year-old Sean Anderson (Josh Hutcherson) is caught by the police after a brief chase on his dirtbike which ended with him driving into a swimming pool while trying to evade them. Minutes later, his stepfather Hank (Dwayne Johnson) arrives where a police officer (Stephen Caudill) who is friends with Hank tells him that Sean had broken into a remote satellite research center. The police officer also tells Hank that he has talked Mr. and Mrs. McGillicutty (the owners of the swimming pool) out of pressing charges. Hank takes Sean home where his mother Elizabeth (Kristin Davis) is not pleased with his actions or the fact that he and Hank don't get along well.
During the end of the Cretaceous era, an Iguanodon mother is forced to abandon her nest during a Carnotaurus attack. The one surviving egg journeys through several predicaments, before ending up on lemur island, where Plio names the hatched baby Aladar and raises him. Years later, Aladar and the lemurs take part in a mating season, where Zini goes without a mate. After the season ends, a meteor strikes and destroys the island, leaving Aladar, Plio, Yar, Zini and Suri, as the only survivors when they swim to the mainland. The family mourns for the loss of all lemurs before moving on.
Slate and Co. Senior Executive Cliff Vandercave (Kyle MacLachlan) and secretary Miss Sharon Stone (Halle Berry) look at the company workers in the gravel pits while discussing their plan to swindle the company of its vast fortune and flee, but decided that they need someone to take responsibility for it. Fred Flintstone (John Goodman) loans his best friend and neighbor Barney Rubble (Rick Moranis) money so that he and his wife Betty (Rosie O'Donnell) can adopt a child named Bamm-Bamm, who can only pronounce his own name. Although the child is initially difficult to control due to being raised by Mastadons, as well as being superstrong, he eventually warms up to his new family. Barney vows to repay his friend, but Fred is visited by his mother-in-law, Pearl Slaghoople (Elizabeth Taylor), who objects to his decision. However, Fred's wife Wilma (Elizabeth Perkins) remains supportive of his decision.
In an alternate timeline in which Earth was never hit by an asteroid and dinosaurs never became extinct, a young Apatosaurus named Arlo loses his father in a tragic accident. One day, Arlo falls into a river and gets knocked out by a rock, finding himself far away from his home. While trying to find a way back to the Clawed-Tooth Mountains, he befriends a human caveboy that he names Spot.
In the timeframe of 10,000 BC, a tribe of hunter-gatherers called the Yagahl live in a remote mountain range in the Urals and survive by killing woolly mammoths, which they call "mannaks". The camp is led by a hunter who has proven his bravery by killing a Mammoth, and taking the White Spear. The people also strongly venerate an elderly woman, called Old Mother. Because of her different appearance to other humans in the village, it is assumed she is a Neanderthal, the "last of her kind", living with the Homo sapiens of the camp.
The film is set in a post-ice age North America, where the local tribesmen believe all creatures are created through the Spirits, who are said to appear in the form of an aurora. Three brothers: Kenai (voiced by Joaquin Phoenix)- the youngest brother, Denahi (voiced by Jason Raize)- the middle brother -and Sitka (voiced by D.B. Sweeney)- the eldest brother, return to their tribe in order for Kenai to receive his sacred totem, a necklace in the shape of an animal. The particular animal it represents symbolizes what he must achieve to call himself a man. Unlike Sitka, who gained the eagle of guidance, and Denahi, who gained the wolf of wisdom, Kenai receives the bear of love, to which he objects, stating that bears are thieves. He believes his point is made a fact when a bear takes some salmon. Kenai and his brothers pursue the bear, but a fight follows on a glacier, during which Sitka gives his life to save his brothers, although the bear survives. Vengeful, Kenai heads out to avenge Sitka. He chases the bear up onto a mountain and kills it. The Spirits, represented by Sitka's spirit in the form of a bald eagle, transform Kenai into a bear after the dead bear's body disappears. Denahi arrives, mistaking Kenai as dead, and believing the bear is responsible, vows to avenge Kenai by hunting it down.
Paleontologist Zack takes his nephew Ricky and niece Jade on a fossil hunt, giving the sullen Ricky his Gorgosaurus tooth while he and Jade go to the fossil bed. Alone, Ricky is met by a talking rook, who morphs into Alex the Alexornis bird, who takes the story back to the Cretaceous period 70 million years ago. Patchi is the smallest of his litter of Pachyrhinosaurus hatchlings, and is often bullied by his large, proud older brother Scowler. Their father Bulldust is the leader of the herd. Patchi is attacked by a Troodon and receives a distinctive hole in his frill when he ventures outside the nest one morning. Alex, serving as Patchi's mentor, tries to help Patchi impress a female Pachyrhinosaurus named Juniper, but her herd soon migrates south without him. Bulldust soon follows suit, moving his herd to the south, but when they try to pass through a dense forest, they are forced to flee when a forest fire erupts. Taking advantage of the chaos, Gorgon the predatory Gorgosaurus attacks the fleeing Pachyrhinosaurus, and while his pack kills their mother and siblings, Patchi and Scowler witness Gorgon killing Bulldust.
Dennis and his friends find a dinosaur bone in his backyard, dubbed by him as the "Dennissaurus". The discovery makes life miserable for everyone, as scientists, reporters, and amusement park operators overrun the neighborhood.
The plot revolves around 16-year-old Ally Hayden (Liz Stauber), the daughter of Dr. Donald Hayden (Peter Horton), a world-famous paleontologist and museum curator. She loves dinosaurs and longs to be able to accompany him to one of the nearby paleontological digs, but her father thinks this is too dangerous and she has to settle for giving museum tours instead.
In the opening scene, Max Anderson (Jean-Michel Paré) is being pursued by a Giganotosaurus. Max then comes across a fissure vent. When he tries to jump across, he falls while calling out the name of his brother. Ten years later, Max's brother volcanologist Trevor Anderson (Brendan Fraser) is visited by Max's son/Trevor's 13-year-old nephew Sean Anderson (Josh Hutcherson). In a box of items that belonged to Max is a book, Journey to the Center of the Earth by Jules Verne. Notes written by Max are found inside the book.