A Carnotaurus hunts a herd of dinosaurs, destroys a Iguanodon nest, and kills a Pachyrhinosaurus. The lone surviving Iguanodon egg is stolen by an Oviraptor, and, after a series of mishaps, arrives at an island inhabited by prehistoric lemurs. Plio, the daughter of lemur patriarch Yar, names the newly-hatched baby Aladar and raises him alongside her daughter Suri, over Yar's initial protestations.

Several years later, a fully grown Aladar watches the lemurs take part in a mating ritual, in which Plio's awkward teenage brother Zini fails to find a female. Moments after the ritual ends, they are interrupted by a meteor crashing into the Earth, creating an explosive shockwave that destroys the island. Aladar and Yar's family flee across the sea to the mainland. Being the only survivors, they mourn their losses, before journeying inland.

While crossing the burnt desert left by the meteor, the group is attacked by a pack of Velociraptor. They escape by joining a multi-species herd of dinosaur refugees heading for the communal Nesting Grounds. After encountering the callous Iguanodon herd leader Kron, they retreat to the end of the line, and befriend the old Styracosaurus Eema, her pet Ankylosaurus Url, and her equally elderly friend Baylene, a Brachiosaurus. The herd travels for days without water to the site of a lake, only to find it seemingly dried up. Kron orders the herd to move on and let the weakest perish, but Aladar stays behind with a struggling Eema. He and Baylene dig until they reach the water table. The rest of the herd follows suit, and Kron's sister Neera, impressed by Aladar's compassion, begins to grow closer to him. However, Kron sees Aladar's increasing popularity as a threat.

Meanwhile, two Carnotaurus have been tracking the herd, and ambush a scouting party led by Kron's lieutenant Bruton. Surviving the attack, a badly wounded Bruton warns of the approaching predators. Ushering the herd away from the lake, Kron deliberately leaves Aladar, the lemurs, the elderly dinosaurs, and the injured Bruton behind, hoping that they will slow their pursuers down. The abandoned group takes shelter in a cave when a rainstorm begins, but the Carnotaurus find them during the night and attack. Fending off the attacking predators, Bruton sacrifices himself to cause a cave-in that kills one of the Carnotaurus, forcing the survivor to retreat.

Venturing deeper into the cave, the group reaches a dead end, causing Aladar to briefly lose hope. Baylene reproaches him for giving up, and uses her strength to smash through the wall, revealing the intact Nesting Grounds on the other side. As the group briefly celebrates, Eema notices that a landslide has collapsed the usual entrance into the valley. Aladar rushes off to warn Kron, who is attempting to force the herd to climb the rubble, unaware of the sheer drop on the other side. Kron sees the warning as a challenge for the position of herd leader and fights Aladar, until Neera intervenes on Aladar's behalf. She and the herd leave with Aladar, but Kron does not follow them.

The surviving Carnotaurus arrives on the scene; Aladar rallies the herd to stand together against it, forcing the outnumbered Carnotaurus to back off. The predator, after noticing Kron's attempts to climb the rocks alone, attacks him i…

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• D. B. Sweeney as Aladar, a brave and compassionate young Iguanodon. He is the adoptive son of Plio, grandson of Yar, nephew of Zini and the older brother of Suri.
• Alfre Woodard as Plio, a wise lemur who cares for her family. She is the daughter of Yar, older sister of Zini, mother of Suri and the adoptive mother of Aladar.
• Ossie Davis as Yar, a lemur with a gruff attitude but a gentle heart. He is the father of Plio and Zini, maternal grandfather of Suri, and the adoptive maternal grandfather of Aladar.
• Max Casella as Zini, a wisecracking and somewhat hapless teenage lemur, who fancies himself a ladies man. He is the younger brother of Plio, son of Yar, and the maternal uncle of Suri and Aladar.
• Hayden Panettiere as Suri, a sweet, fun-loving young lemur. She is Aladar's adoptive younger sister, Plio's daughter, Zini's niece, and Yar's granddaughter.
• Samuel E. Wright as Kron, Neera's brother and the Iguanodon leader of the herd of survivors. He behaves as a Social Darwinist, only concerned about the "fit/strong" dinosaurs and his own position as leader.
• Julianna Margulies as Neera, a kindly, sensible Iguanodon who is Kron's sister and Aladar's love interest.
• Peter Siragusa as Bruton, Kron's harsh and fatalistic Iguanodon lieutenant who softens once Plio helps heal his injuries.
• Joan Plowright as Baylene, an elderly, dainty and friendly Brachiosaurus, who is the last known of her kind after the meteor. Chris Farley was originally slated to voice the character, when it was originally written as a male character named Sorbus. After his death, the character was rewritten as a female.
• Della Reese as Eema, a wizened, elderly and slow-moving Styracosaurus with a comically snarky demeanor.
• Michael T. Weiss as Creto, an Iguanodon scout who is killed by the two Carnotaurus.

The film's score was composed by James Newton Howard with choral directing by Lebo M, who did vocals for The Lion King (1994). In September 1999, it was reported that pop singer/songwriter Kate Bush had written and recorded a song for the film to be used in the scene in which Aladar and his family mourn the destruction of their island. Reportedly, preview audiences did not respond well to the song. The producers recommended that Bush rewrite it, but she refused. Ultimately, due to complications, the track was not included on the soundtrack.

The soundtrack album was released on May 5, 2000, by Walt Disney Records. Howard would later compose the scores for the Disney animated features Atlantis: The Lost Empire (2001), Treasure Planet (2002), and Raya and the Last Dragon (2021). One track, "The Egg Travels", was heard in many trailers following the film's release, including Lilo & Stitch (2002), The Wild Thornberrys Movie (2002), and Around the World in 80 Days (2004).

While the film got mixed reviews from critics, the film score received universally positive critical reception, with critics singling out "The Egg Travels" in particular as one of the best. For his work, James Newton Howard was nominated for an Annie Award for Music in a Feature Production and Saturn Award for Best Music.