After visiting the Land of Dragons and Beast's Castle, Sora, Donald, and Goofy suddenly feel a mysterious force which pulls the Gummi Ship back to Hollow Bastion. They see some Heartless emerging from Merlin's house. Inside, the wizard tells them that he found Winnie the Pooh's storybook. He says that Leon and the others need to know first, so he vanishes to go find them, but Sora can't wait to see Pooh again, so he immediately leaps into the book.
Inside the book, Sora finds Pooh in front of his house, sitting on a log. He offers to let him join in on his "stoutness exercises," but when he jumps off the log, he suddenly freezes in time. When Sora tries to touch him, a blast of wind suddenly boots him out of the book. Back outside, Donald and Goofy call him to help them. He goes out but forgets the book, allowing some other Heartless to grab it. They manage to defeat the Heartless, but the book gets torn. Sora reenters it, and everything seems normal at first, but then Pooh forgets both Sora and all his friends. Sora goes back outside to Merlin, who explains that he'll have to find the book's torn pages again to restore Pooh's memories. He gives Sora a new summoning ability before sending them off.
After finding some pages, Sora returns to the 100-Acre Wood. He sees Gopher, who warns Pooh that it's Windsday, so he needs to leave before the wind blows him away. When Sora arrives, he sees that Piglet has been picked up by the wind. He and Pooh help Piglet get down after he gets stuck in a tree, and Pooh manages to recall Piglet's name. Unfortunately, though, he still doesn't remember Sora.
Next, Sora and Piglet find Pooh floating with a balloon, about to crash on top of Eeyore's house. They try to stop him, but it's too late. They decide to give him some honey, hoping that that will jog his memory. They find Rabbit's house, which is full of honey, and Pooh proceeds to eat it, but he can't remember anything else. He tries to go through the hole in Rabbit's house, but he gets stuck once again. After the gang pulls him out, he manages to remember Rabbit and Eeyore, but not Sora.
After that, Sora heads for Kanga and Roo's house, where Kanga has made some medicine to restore Pooh's memory. Before they can use it, however, Tigger comes along and takes it. He says that bouncing is more likely to make him remember than medicine, but it doesn't work. Tigger throws the bottle of medicine in frustration, which causes Pooh to remember him. That night, Pooh has a dream in which he recalls Sora leaving the 100-Acre Wood during his first adventure, but he still can't remember Sora's name.
Sora finds his way to an ominous cave where all of Pooh's friends are waiting. They tell Sora that the bear has gotten lost inside, but they need his help to brave the dangers of the cave. Together, they venture deep inside and find Pooh. He says that he was looking for a close friend he made a promise to. After being tackled by Tigger and having his tummy rumble, Pooh finally remembers Sora's name.
Later, Sora heads to a starry hill, where Pooh has gotten his head stuck in a honey pot. He helps him get it free before asking him what he was doing. Pooh says that he was trying to find a way to stop Sora from leaving. Sora tells him that he'll always be with him in his heart. Pooh and all his friends say goodbye to Sora, and he leaves the book. As he does, the worn-out old cover is replaced by a new one of the older Sora and Pooh looking out into the starry sky...
