In 3067 BC, the Scorpion King leads his army on a campaign to conquer the world. Seven years later, the Scorpion King and his army are defeated and exiled to the desert of Ahm Sher. His men die of heat exhaustion, leaving only the Scorpion King. Vowing to give Anubis his soul for the power to defeat his enemies, an oasis is created to hide the Scorpion King's pyramid and giving him a legion of humanoid jackal warriors to seek revenge. The Army of Anubis sweeps across Egypt, destroying everything in its path, but once their task is finished Anubis claims the Scorpion King's soul and his army.
In 1933, Sora and friends, Rick and Evelyn O'Connell explore a ruined mortuary structure in the ancient Egyptian city of Thebes with their son, Alex. They find the Bracelet of Anubis. In London, Alex puts on the bracelet, which shows him a vision with directions to the Oasis of Ahm Shere. Alex has seven days to reach the oasis, or the bracelet will kill him the moment the sun's rays shine on the Scorpion King's pyramid; at that point, the Scorpion King and his army will reawaken.
Evelyn, Cindy, Sawyer, Minnie, Rebecca and Perdita are captured by an Egyptian cult who have resurrected Imhotep; they wish to use Imhotep's power to defeat the Scorpion King, which would give him command of Anubis' army to take over Earth. The cult, led by Baltus Hafez, the British Museum's curator, includes a warrior named Lock-Nah and Meela Nais, the reincarnation of Imhotep's love Anck-su-namun. Pooh and friends and the O'Connells set out to rescue her, accompanied by Evelyn's brother Jonathan, Carter Grayson, Dana Mitchell, Chad Lee, Joel Rawlings, Kelsey Winslow, Ryan Mitchell, Wesley Collins, Jen Scotts, Lucas Kendall, Trip, Katie Walker, Eric Myers and the Medjai Ardeth Bay.
After having discovered the bracelet is missing, they attempt to kill Evelyn, however a fight ensues between Rick and Imhotep. Imhotep then calls on the help of his mummified soldiers to kill them. After freeing Evelyn they flee on a double-decker bus. After defeating them, Alex, Pooh, Pongo, Scooby, Baloo, Yogi, Kit, Molly, Hunter, Blitz, Pep, Tiger, Spike, Ducky, Petrie, Mr. Peabody, Odette, Faline, Pluto, Dinah and Lulubelle are kidnapped and they travel across Egypt to rescue him along with Rick's associate from his past adventures, Izzy, a pilot, who provides the group with transportation. In the third of a train, Pooh, Yogi, Baloo, Pongo, Hunter, Blitz, Tiger and Scooby are pushed by Imhotep and are confronted by Kaa, Arthur and Cecil, Brer Fox, Brer Bear and the Grand Duke of Owls. They tell them that they been sent to wake Imhotep. Kaa hypnotizes Yogi, Hunter, Blitz, Baloo, Scooby, Pongo, Tiger and Pooh to sleep.
The bracelet gives Alex visions, directions to Ahm Shere that the cult follows. At each location, Alex leaves clues for his parents and their friends who follow in Izzy's dirigible. Imhotep uses the Book of the Dead to give Meela Nais the soul of Anck-su-namun but by doing so he allows Evelyn to unlock the memories of her previous life as Princess Nefertiri, the bracelet's keeper and Pharaoh Seti I's daughter. Lock-Nah discovers that Alex has been leaving clues, so Imhotep makes a wall of water that attacks the dirigible. The heroes and the O'Connells crash in the jungle of Ahm Shere. Izzy stays with the dirigible in hopes of repairing it. The heroes and the O'Connells attack the cult, and both groups are attacked by pygmy mummies. Rick retrieves Alex while Ardeth Bay kills Lock-Nah. Pooh, Yogi, Baloo, Hunter, Blitz, Scooby, Tiger and Pongo are rescued by Krypto, Colleen, Exile, Rat, Mole, Copper, and Tigger and are wake up from the hypnosis. Putt-Putt, Bongo, Mickey, Donald, Goofy, Bambi, Simba, Timon, Pumbaa, Rabbit and Piglet rescue Lulubelle, Mr. Peabody, Odette, Faline, Spike, Ducky, Petrie, Kit, Molly, Pluto, Dinah and Pep. They escape from the pygmies, who kill most of the cult except for Baltus. Imhotep and Anck-su-namun are unharmed due to Imhotep's powers and Anck-su-namun being the keeper of the Book of the Dead.
Rick and Alex run to the pyramid, barely making it before sunrise. The bracelet detaches from Alex's arm. Ardeth regroups with the Medjai in case Anubis' army rises. Anck-su-namun stabs Evelyn and kills her. Rick, grieving, pursues Imhotep. Baltus puts on the bracelet and revives the army. As Imhotep walks into the pyramid, Anubis takes his powers, wanting Imhotep to fight as a mortal. Pooh, Tigger, Piglet, Baloo, Benjamin, Stitch, Pongo, Perdita, Bambi, Yogi, Boo-Boo, Princess Paw, Danny, Mickey, Pluto, Donald, Goofy, Sora, Bongo, Stitch, Brer Rabbit, Llttlefoot, Cera, Spike, Ducky, Petrie, Chomper, Ruby, Fievel, Tiger, Tod, Copper, Lucky, Cookie, Niblet, Squirt, Strudel, Mr. Peabody, Krypto, Fred, Daphne, Velma, Shaggy, Scooby, Louis, Tantor, Terk, Genie, Jiminy, Zazu, Kronk, Olaf, Hunter, Colleen, Exile, Blitz, Putt-Putt, Rick and the Vultures find Imhotep, Duke of Owls, Kaa, Arthur and Cecil, Brer Fox, Brer Bear and the villains summoning the Scorpion King and they fight. The Medjai engage the army. The Scorpion King interrupts Rick and Imhotep, the heroes and villains' fight. The heroes realize that the Scorpion King is Mathayus. Imhotep tells the Scorpion King that he is the Scorpion King's slave, but Rick was sent to kill him. During Rick and the Scorpion King's fight, Baltus is killed. Rabbit, Eeyore, Rat, Mole, Cindy, Rebecca, Mary Poppins, Odette, Faline, Minnie, Dinah, Sawyer, Shag, Kit, Molly, Pep, Jonathan and Alex collaborate to steal the Book of the Dead from Anck-su-namun. Alex uses the book to resurrect Evelyn, who duels with Anck-su-namun. Mary Poppins and Odette watch Jonathan fighting Anck-su-namun. In a direct reference to the first film, Alex asks Jonathan for help to decipher a hieroglyph; the same hieroglyph Evelyn had to translate for Jonathan in first film.
Cindy, Minnie, Sawyer, Rebecca, Odette, Faline, Dinah, Mary Poppins, Rabbit, Kit, Molly, Sherman, Rat, Mole, Pep, Shag, Eeyore, Alex and Jonathan go help Rick while Evelyn fights Anck-su-namun. It is revealed that the scepter that Jonathan has been carrying extends into a spear that can kill the Scorpion King. Tigger uses his boomerang to defeat Brer Fox and Brer Bear. Sora tells Jafar to go back into his own lamp and Jafar disappears into the lamp. Yogi throws and defeats Kaa. Putt-Putt uses his flashlight to defeat Duke of Owls. Mickey and Sora fight Maleficent. The Medjai seemingly defeat Anubis' army despite heavy casualties, but see that they have only defeated the vanguard, and the full army is charging towards them. However, before the Anubis warriors hit the Medjai lines, Rick succeeds in killing the Scorpion King, sending him and his army back to the Underworld. The Scorpion King's death breaks his oath with Anubis, causing the oasis to turn back into a desert, and the oasis to be sucked into the pyramid. Rick and Imhotep are hanging from the edge of a pit that leads into the underworld. Evelyn risks her life to save Rick, but Anck-su-namun refuses to do the same for Imhotep, and abandons him. Heartbroken about her desertion, he lets go of the ledge, falling into the underworld, to his death. Anck-su-namun, running away from the pyramid, falls into a pit of scorpions and flesh-eating scarab beetles.
The heroes and the O'Connells reach the top of the pyramid, which is being sucked into the desert. Elliot appears and Izzy arrives with a modified dirigible and they save the heroes and the O'Connells. Jonathan grabs the diamond at the top of the pyramid. Ardeth Bay salutes them as they fly over him.
- The Story of The Scorpion King
- Inside Thebes
- Outside the Ruins of Hamunaptra
- Home in London
- Kidnapping Evelyn, April and Jessie
- Rescuing the Girls
- Kidnapping Alex, Pooh and friends
- Inside the trian
- The Balloon Ride
- Finding Clues
- Entering the Jungle
- Rescue of Alex, Pooh and friends
- Reaching the Pyramid
- Killing the Scorpion King
- Evacuating the Pyramid
- Happy Ending
- Pongo and Perdita, Krypto, Rebecca Cunningham, Kit Cloudkicker, Molly Cunningham, Scooby-Doo, Shaggy Rogers, Fred Jones, Daphne Blake, Velma Dinkley, Simba, Timon, Pumbaa, Louis, Tantor, Terk, The Vultures, Jiminy Cricket, Zazu, Kronk, Lucky, Cookie, Niblet, Squirt, Strudel, Littlefoot, Cera, Spike, Petrie, Ducky, Chomper, Ruby, Fievel Mousekewitz, Tiger, Arthur and Cecil and The Evil Schemers will guest star in the film.
- Music from Titanic (composed by James Horner), Pinocchio (composed by Leigh Harline), Dumbo (composed by Oliver Wallance), Spider-Man (composed by Danny Elfman), Ice Age 2: The Meltdown (composed by John Powell) and Star Wars Episode 1: The Phantom Menace (composed by John Williams) will be used in all scenes.
- An American Tail series, The Land Before Time series and The Mummy Returns are made in Universal Pictures.
- Genie, Olaf, Oscar (Pig), Kate (Fox) and Martin will make their debut.
- In the scene, Kaa sing Trust In Me when he captures Pooh and the gang to be hypnotized.
- The storyline continues in Pooh's Adventures of The Mummy 3: Tomb of the Dragon Emperor.
- The film takes place after Littlefoot vs The Mummy (which explains that Littlefoot and friends met Rick O'Connel, Evelyn, Jonathan and Ardeth Bay and faced Imhotep).