Woody prepares to go to cowboy camp with Andy, but when Woody's right arm gets ripped accidentally, Andy puts him on a shelf and leaves without him. The next day, Woody finds Wheezy, a penguin squeaky toy, has been shelved for months due to a broken squeaker. Andy's mother puts Wheezy in a yard sale, but Woody rescues him, only to be stolen by a greedy toy collector, who takes him to his apartment. Buzz Lightyear and all of Andy's toys identify the thief from a commercial as Al McWhiggin, the owner of a toy store called Al's Toy Barn. Buzz, Hamm, Mr. Potato Head, Slinky Dog, and Rex all set out to rescue Woody.
At Al's apartment, Woody learns that he is a valuable collectable based on a 1950s TV show called Woody's Roundupand is set to be sold to a toy museum in Tokyo, Japan. While the toys from the show—Jessie, Woody's horse Bullseye, and Stinky Pete—are excited about going, Woody intends to return home since he is still one of Andy's toys. Jessie is upset because the museum is only interested in the collection if Woody is in it, meaning they will return to storage if he is absent from the collection. When his arm is torn off completely, Woody attempts to retrieve it and escape but is foiled when Al's television set turns on. Woody finds the TV remote in front of Jessie's display case and believes she is responsible. The next morning, a toy repair specialist fixes his arm, and Woody learns that Jessie once belonged to a child named Emily, who eventually outgrew her and gave her away. Stinky Pete warns him that the same fate awaits him when Andy grows up, whereas he will last forever in the museum. Woody decides to stay, now believing that all toys will eventually get discarded by their owners.
Meanwhile, Buzz and the other toys reach Al's Toy Barn. While searching for Woody, Buzz is imprisoned in a cardboard boxby another Buzz Lightyear action figure, who still believes he is a real space ranger. New Buzz joins the other toys, who mistake him for their Buzz. After discovering Al's plan, they arrive at his apartment while Andy's Buzz escapes and pursues them, accidentally freeing an Emperor Zurg toy, who immediately goes after him with the intent of destroying him. After the toys find Woody, Buzz rejoins them and proves that he is Andy's Buzz, but Woody refuses to go home. Buzz reminds Woody that a toy's true purpose is to be played with, which he would never experience in a museum. After seeing a boy play with him on TV, Woody changes his mind and asks the Roundup toys to come with him. Pete refuses and prevents the gang's escape; having never been taken out of his box and played with, he wants to go to the museum where he will be appreciated forever. Al then returns, packs the gang in a case for transport, and leaves for the airport.
Andy's toys follow Al, but are caught by Zurg, who battles New Buzz until Rex knocks him off the elevator, injuring him. New Buzz then chooses to remain behind with Zurg. Accompanied by three toy Aliens, Andy's toys steal a Pizza Planet delivery truck and follow Al to the airport, where they enter the baggage handling system and free Woody. Stinky Pete rips Woody's arm with his pickaxe and threatens him, but Andy's toys stuff him into a little girl's Barbie backpack. They free Bullseye, only for Jessie to end up on the plane bound for Japan. Assisted by Buzz and Bullseye, Woody frees Jessie and the toys find their way home.
When Andy returns from camp, he accepts Jessie, Bullseye, and the Aliens as his new toys, thinking his mother bought them, and repairs Woody's torn arm. Meanwhile, Al's business has suffered due to his failure to sell the Roundup toys. Woody tells Buzz that he is not worried about Andy discarding him because, when he does, they will still have each other for company. Wheezy's squeaker has been fixed and he sings "You've Got a Friend in Me".
- Peter Griffin, Natsu Dragneel, Lucy Heartfilia, Erza Scarlet, Gray Fullbuster, Wendy Marvell, Happy, and Carla guest star in this film.
- Brian will be taken with Woody by Al, while the Eeveelutions, Peter, and Team Natsu will be with Buzz, and the rest of the gang to rescue them.
- The storyline continues in Brian and the Eeveelution Family's Adventures of Toy Story 3.
- Opening Scene/Buzz's Mission
- Woody's Lost Hat/Woody's Arm rips
- Woody's Nightmare
- Woody Finds Wheezy/Yard sale!
- Kidnapped!/Who Stole Woody and Brian?
- Woody meets the Roundup gang/Operation, Rescue Woody and Brian!
- Back at the Penthouse/Woody loses his arm
- With the rescue team/Woody retrieves his arm
- Crossing The Road/The Cleaner arrives
- In The Toy Barn/Woody's Restoration
- The Buzz Lightyear isle/The Barbey isle/Buzz swap
- Jesse's Story
- In Al's office/Buzz escapes
- Into the vents/up the elevator shaft
- To the rescue/Woddy Stays
- Stinky Pete's true colors/It's Zurg!
- Pizza Planet Truck Pursuit
- In the Airport/Woody vs Stinky Pete
- Saving Jeese/Back home
- Woody's arm fixed/"You've Got a Friend in Me"