The film opens with an Iguanodon mother forced to abandon her nest, with only one egg surviving a Carnotaurus attack. The egg eventually ends up in an island inhabited by Smilodectes, who see the egg hatch, name the baby dinosaur Aladar, and raise him as their own. When Aladar is an adult, he meet Winnie the Pooh, Piglet, Tigger, Rabbit, and Eeyore, who were on their way to revisit The Great Valley to see Littlefoot and his friends again. Later, the island is destroyed when an asteroid crashes on Earth, causing a violent meteor shower, with only Aladar, his grandfather Yar, his mother Plio, his best friend Zini and his sister Suri surviving the destruction of the island by swimming to the mainland.
After fleeing a pack of Velociraptor, the family meets a multi-species herd of dinosaurs (consisting of a bunch of Iguanodon, Styracosaurus, Pachyrhinosaurus, Stygimoloch, Microceratops, Parasaurolophus, and Struthiomimus) led by the Iguanodon Kron and his lieutenant Bruton the Altirhinus, who are on a journey to reach the "Nesting Grounds", a valley believed to be untouched by the devastation of the asteroid impact. Aladar and the lemurs befriend a trio of elderly dinosaurs: Baylene the Brachiosaurus, Eema the Styracosaurus, and Url, Eema's dog-like pet Ankylosaurus. Aladar also develops romantic feelings for Kron's sister Neera, but she appears uninterested. Meanwhile, the Velociraptor pack continues to follow them, but are scared off when a pair of Carnotaurus also pick up the herd's trail.
The herd arrives at a lake they have relied on for past trips, but it has dried up, due to the meteor shower from earlier. Aladar saves the herd from dehydration when he and Baylene eventually dig up the trapped water beneath the ground, though Kron claims the water for himself. Aladar and Neera eventually fall in love after Neera sees Aladar helping the dinosaurs (especially the elderly ones) survive. However, Bruton, having been sent by Kron to find water upon arrival at the lake, returns injured by the Carnotaurus which killed another Iguanodon that was scouting with him. Kron evacuates the herd from the lake bed in a rush, leaving Aladar, the lemurs, the elderly dinosaurs and the injured Bruton behind. When Aladar tries to slow the herd, Kron pushes him away and warns Aladar that he will be killed if he interferes with his leadership again. Neera wants to help Aladar but Kron forces Neera to leave him.
The small group recuperates in a cave during a rainstorm, with Bruton eventually befriending them. When the Carnotaurus pair attacks, Bruton proves his loyalty when he holds them off to ensure their escape and kills one of them as the others escape to the depths of the caves, dying in the process. Badly injured, the other Carnotaurus escapes, enraged by the death of its mate but unable to follow the group. Upon reaching a dead end, Aladar begins to lose hope, after repeated failures and the loss of Bruton. However, Zini smells fresh air, and finds the dead end to actually be a blocked exit that is hard to break down. His friends all join in breaking down the barrier, stabilizing his confidence. Finally, Baylene demolishes the wall. The exit actually leads to the "Nesting Grounds", although Eema sees that the old entrance – where the herd has gathered on the other side – has been blocked by a landslide generated by the meteors.
Knowing that the herd will not survive the sheer drop from climbing over it, Aladar rushes to find the herd on the other side, accidentally alerting and being tracked by the Carnotaurus. He finds the herd being directed by Kron to climb the rocks, which cannot be passed without fatality, but when he suggests the alternate route he found, Kron becomes enraged at his authority being questioned and challenged, and attempts to kill Aladar to try and take back his leadership. Aladar is outclassed by Kron, who only stops short of killing Aladar when Neera, now fed up of her brother's illogical beliefs, strikes him down and defends Aladar, effectively desolving Kron's power as leader. Aladar and Neera take control of the herd, but Kron refuses to submit to the leadership of another and begins climbing the rocks himself.
The fight between Aladar and Kron proves to be a huge delay, as the Carnotaurus then confronts them, but Aladar rallies the herd to stand together against their longtime enemy. The Carnotaurus, overpowered, is forced to let the herd pass but spots Kron trying to climb the rocks alone and charges him as easy prey, followed by Neera and Aladar. In the ensuing fight, Kron is trapped at the edge of a precipice and severely wounded by the Carnotaurus, but Aladar is able to push the predator off the cliff to its death. Kron, however, succumbs to his injuries and dies with Aladar and Neera at his side.
Aladar and Neera lead the herd back to the "Nesting Grounds" through the cave, where the two eventually mate and have children, and the lemurs find more of their own kind. Plio narrates the ending, wishing for their story to be remembered in history. She then says, "But one thing is for sure. Our journey is not over, we can only hope in some small way our time here will be remembered".
- The Vultures (Buzzie, Flaps, Dizzy, and Ziggy) and Jiminy Cricket will join Pooh and his friends in Daniel Esposito's upcoming remake version of this film, making it the official debut of Jiminy Cricket and taking place after Winnie the Pooh Meets Pinocchio.
- This is DisneyAnimeManiac's second and final crossover with computer-animated film; the first being Pooh's Adventures of A Bug's Life.
- DisneyAnimeManiac's original version was a PAL film with PAL bits from Pooh's Grand Adventure: The Search for Christopher Robin and Piglet's Big Movie and NTSC bits from The Many Adventures of Winnie the Pooh, The Tigger Movie, and Pooh's Heffalump Movie. However, Daniel Esposito's upcoming remake version will be an NTSC film with NTSC bits from the Winnie the Pooh films, The Jungle Book 1 and 2, Pinocchio, Fun and Fancy Free, Mickey's Christmas Carol, and Mickey's Magical Christmas: Snowed in at the House of Mouse.
- In both versions of this film, Littlefoot is mentioned twice in this film. He is mentioned at the beginning of the film when Pooh and his friends are on their way to visit The Great Valley again to see him and his friends. Later, Littlefoot is mentioned again alongside Cera by Eema, revealing them to be grandparents of Baylene and Eema and realizing how long it had been since she last heard the name "The Great Valley", when Pooh noticesd that the Nesting Grounds looks like The Great Valley. However, Pooh and his friends are time travelers, so they will see Littlefoot and his friends again in Pooh's Adventures of The Land Before Time II: The Great Valley Adventure.
- Both The Tigger Movie and Dinosaur were released in 2000.
- The Winnie the Pooh series, The Jungle Book, Pinocchio, and Dinosaur were all made by Disney.