Ten years have passed since the invasion of Naboo, and the Galactic Republic is experiencing a crisis. Former Jedi Master Count Dooku has organized a Separatist movement against the Republic, making it difficult for the Jedi to maintain the peace. The Republic contemplates creating an army to assist the Jedi, prompting Senator Padmé Amidala, former Queen of Naboo, to return to Coruscant with Winnie the Pooh, Piglet, Tigger, Rabbit, Eeyore, the Good Fairy, Mewtwo, Slimer, Stay Puft, Ash Ketchum, Misty Waterflower, Brock, Pikachu and Togepi to vote on the matter. Upon there arrival, they narrowly escape an assassination attempt. Shaken by the close call, Supreme Chancellor Palpatine assigns Jedi Knight Obi-Wan Kenobi and his apprentice Anakin Skywalker to protect them. That night, another attempt on the Senator's life is made, though Obi-Wan and Anakin foil the plot and subdue the assassin, who is permanently silenced by her mysterious employer when the Jedi force her to reveal vital information. Returning to the Jedi Temple, Obi-Wan is assigned to investigate the identity of the assassin's killer with Mewtwo, Piglet, The Good Fairy, Slimer, Stay Puft, Ash, Misty, Brock and Pikachu while Pooh, Tigger, Rabbit and Eeyore are stuck with Anakin who is assigned to escort and accompany Senator Amidala to her homeplanet of Naboo. Anakin, who has grown infatuated with Padmé, relishes the opportunity to spend time with her as Pooh and the other 3 stuffed animals suspect matchmakeing, though Padmé resists her feelings toward him, as that would go against the moral codes of their careers as a Jedi and a senator, respectively.
Obi-Wan and company's investigation leads them to the remote planet of Kamino, where they discovers that an army of clones is being secretly produced for the Republic. Obi-Wan deduces the clones' template, a bounty hunter named Jango Fett, is the killer he's looking for. After unsuccessfully trying to capture him, Obi-Wan tracks him down to the planet Geonosis. Anakin, meanwhile, has grown troubled with recurring nightmares about his mother, whom he had left behind on Tatooine when he set off to become a Jedi, in grave danger. In defiance of his orders to remain on Naboo, Anakin convinces Pooh, Padmé, Tigger, Rabbit and Eeyore to accompany him to Tatooine to free his mother. There he finds her abducted and beaten by Tusken Raiders, and she dies in his hands. Anakin reveals his true nature cold and cruel, slaughtering the entire Tusken community in tears ("i don't suppose you be statisfied with a hug instead" comments Pooh in a deleted scene as in the final version it is Tigger who says "Poor guy, his very little brain has half gone with grief" ).
On Geonosis, Obi-Wan and company learn it was Count Dooku who authorized the assassination attempt on Senator Amidala and Pooh's group, and that the Separatists are in development of a new droid army. Obi-Wan relays this information via hologram to Anakin, who transmits it to the Jedi Council, though Obi-Wan and company is captured mid-transmission. While Anakin and Padmé head to Geonosis to rescue Obi-Wan, Chancellor Palpatine is granted emergency powers to organize the clone army and send them into battle. Shortly after arriving on Geonosis, Anakin, Pooh, Tigger, Rabbit, Eeyore and Padmé are captured and sentenced to death along with Obi-Wan. Preparing for what could be their final moments, Padmé finally reveals her feelings for Anakin and they share (what they believe to be) one last kiss. The group are pitted against savage beasts, though they manage to hold their own before Jedi Master Mace Windu arrives with a team of Jedi to assist them, engaging and decapitating Jango Fett in the brief battle. After a heated struggle, Jedi Master Yoda arrives with the clone army and collects the surviving Jedi.
As a large battle erupts between the Republic's clone army and the Separatist's droid forces, Count Dooku attempts to escape. Obi-Wan and Anakin corner him in a hangar and engage him in a lightsaber duel, but he outmatches and defeats them with his mastery of the dark side of the Force, ampulating Anakin's hand in the process. Yoda engages Dooku in a fierce duel, though Dooku manages to escape once more, taking the plans for a new "ultimate weapon" to his Sith master on Coruscant. The Jedi are now uncertain of what will become of the Republic, now that the Clone Wars have begun. Chancellor Palpatine oversees the launching of massive clone trooper forces. Meanwhile, Anakin, with a new golden hand, privately marries Padmé on Naboo with R2-D2, C-3PO and Pooh and gang (along with a few more guest stars) as witnesses.
- Good Fairy
- Stay Puft
- Ash Ketchum
- Misty Waterflower
- Team Rocket (Jessie, James and Meowth)
- Bowser Jr.
- Mistress Nine
- Pooh and friends have not aged a day in the ten year gap between the films. This is because the Good Fairy's magic has made them impervious to space aging.
- From the point that Anakin goes with Padme to Naboo while Obi-Wan investigates the saberdart, Pooh's group splits up. Pooh, Eeyore, Tigger and Rabbit travel with Anakin while the rest of the group travel with Obi-Wan.
- When Team Rocket capture Obi-Wan's group on Geonosis initially, they interrupt his recording saying that he and his friends have been captured, taunting the Jedi.
- When Dooku and Team Rocket return to Sidious in The Works, they are contacted by Bowser and his family, who is planning to leave a message for Pooh and friends in Neverland. The Clone Army intercept this message and show it to Mewtwo, so Mewtwo arranges an immediate shuttle for Earth.