The movie is also the first Winnie the Pooh film (and the first Disney direct-to-video film) ever to have its special edition never have a VHS release and be only on DVD. It was not given an American rating, but in Canada it holds a G-rating.
Once upon a last day of a golden summer, Christopher Robin does not have the heart to tell Winnie the Pooh of his departure to school the next day. Although the two have fun playing the whole day, Christopher Robin is unable to tell Pooh where he's going, and leaves him with the advice, "You're braver than you believe, stronger than you seem, and smarter than you think." The next morning, Pooh discovers a honey pot with an attached note - however, he cannot read it himself. As he goes around to his friends Piglet, Tigger, Rabbit and Eeyore, it's clear that the group needs Christopher Robin's help and advice with their own obstacles, and none of them are able to read it. From reading the note, Owl reports that Christopher Robin has been taken to a distant, mysterious and dangerous land called Skull against his will. Owl equips the group with a map and sends them into the "Great Unknown" of the Hundred Acre Wood, warning them of the ferocious beast that lords over Skull, the "Skullasaurus".
Soon after their departure, growls are heard off into the distance, and the group assumes that they are being pursued by the Skullasaurus. This causes all out panic and, being a "bear of very little brain", Pooh quickly proves unfit for leading his friends on this mission, leading Rabbit to assume command of the five. During their travels the group slowly realizes just how helpless they are without Christopher Robin in the outside world: In a tranquil valley outside of a forest of thorns, Piglet is abducted by a swarm of butterflies, making him believe he is too afraid to do anything; at a ravine, Tigger doesn't have the strength to bounce out to safety, causing all his friends to plummet with him in their attempt to retrieve him; and finally, Rabbit realizes he is helpless with the map ripped in two, leaving the group lost in the mist. The group comes to terms with the fact that they are lost and helpless without Christopher Robin, but take shelter in a nearby cave. While everyone is asleep, Pooh, heartbroken, laments getting no closer to finding his dear friend Christopher Robin.
In the morning, the five realize with horror that they took refuge in Skull Cave itself, the perilous den of the Skullasaurus. Though very much afraid, the five all split up to search for Christopher Robin on their own; however, the Skullasaurus' roars and growls eventually herd Piglet, Tigger, Rabbit and Eeyore together, who, mistaking Pooh's monstrously distorted reflection in a huge crystal to be the Skullasaurus, flee without Pooh. The bear becomes stuck in a narrow crevasse in the cave's crystals, and his muffled cries make the other four believe he has been killed and eaten by the Skullasaurus. Seeing the entrance to the "Eye of the Skull", where Christopher Robin supposedly is, the remaining four decide to push on for Pooh's memory, and are able to prove their potential: Rabbit proves his intelligence by devising a plan to reach the top, Tigger proves his strength by bouncing up there unassisted, and Piglet proves his bravery by getting Rabbit and Eeyore a way up to the ledge. Pooh has been watching this the whole time, and excitedly frees himself, only to hit a rock wall and descend into a deep pit, with no way out. While in despair at his permanent imprisonment, Pooh deduces that Christopher Robin is still with him in his heart, and it is enough to get the bear out of his sadness.
The others reach the Eye of the Skull, and indeed find Christopher Robin alive and well, but explain that Pooh was seemingly killed by the Skullasaurus. Upon hearing the creature's roars again, Christopher Robin explains that they are only the growls of Pooh's stomach (Pooh had never eaten any of his honey because he had intended on saving it for when he found Christopher Robin), and explains he had to go to school not Skull, and he would return in the afternoon. Rabbit realizes that Owl was only joking. Christopher Robin rescues Pooh from the deep pit, much to the bear's joy.
The six exit Skull Cave, only to discover that from the outside, it is far less frightening then when they first arrived. Christopher Robin explains that since they were alone and afraid, it only appeared to be huge and menacing, and this proves true for all the obstacles they'd faced on their journey as they happily march home. That evening, Christopher Robin says he will return to school, but that they have no need to embark on another quest to find him, since he will always return. Pooh declares that he will always be waiting for him, and the two happily watch the sunset, knowing they will always have each other in the sanctuary of the Hundred Acre Wood.
- Jim Cummings - Winnie the Pooh / Skullasaurus growls
- Ken Sansom - Rabbit
- John Fiedler - Piglet
- Paul Winchell - Tigger
- Peter Cullen - Eeyore
- Brady Bluhm - Christopher Robin
- Andre Stojka - Owl
- Frankie J. Galasso - Christopher Robin (singing voice)
- Narrated by David Warner