In 3067 BC, the Scorpion King leads his army on a campaign to conquer the world. Seven years later, his army is defeated while attacking Thebes and exiled to the desert of Ahm Shere, where his men die of heat exhaustion. After vowing to give Anubis his soul for the power to defeat his enemies, an oasis forms to hide the Scorpion King's pyramid and he receives a legion of jackal warriors. The Army of Anubis sweeps across Egypt, but once their task is finished, Anubis claims the Scorpion King's soul and his army.
In 1933, Rick and Evelyn O'Connell explore a ruined mortuary temple in ancient Thebes with their son, Alexander, where they find the Bracelet of Anubis. In London, the bracelet locks onto Alex, showing him a vision directing him to Ahm Shere. Alex has seven days to reach the oasis before the bracelet will kill him when the sun's rays shine on the Scorpion King's pyramid.
Evelyn is captured by an Egyptian cult who resurrect Imhotep; they wish to use his power to defeat the Scorpion King, giving him command of Anubis's army to take over the world. The cult, led by Baltus Hafez, the British Museum's curator, includes a warrior named Lock-Nah and Meela Nais, the latter being a reincarnation of Imhotep's lover Anck-su-namun. Rick sets out to rescue Evelyn, accompanied by her brother Jonathan and the Medjai Ardeth Bay.
Hafez attempts to sacrifice Evelyn but a fight ensues between Rick and Imhotep. Imhotep awakens mummified soldiers to kill Rick and the others. Freeing Evelyn, they flee on a double-decker bus. Alex is kidnapped by Lock-Nah, and along with the cult travels to Egypt. The O'Connells pursue along with Rick's associate from past adventures, Izzy, a pilot who provides the group with transportation.
The bracelet gives Alex directions to Ahm Shere and they travel there by train. Alex leaves clues for his parents, who follow in Izzy's dirigible. Imhotep uses the Book of the Dead to give Meela Nais the soul of Anck-su-namun, but inadvertently allows Evelyn to recover her memories of her previous life as Princess Nefertiri, the bracelet's keeper and Pharaoh Seti I's daughter. Lock-Nah finds Alex leaving clues, so Imhotep makes a wall of water that attacks the dirigible, causing the O'Connells to crash into the jungle of Ahm Shere. Izzy stays with the dirigible to repair it. The O'Connells attack the cult, and both groups are attacked by pygmy mummies. Rick retrieves Alex while Ardeth Bay kills Lock-Nah. They escape the pygmies, who kill the cult except for Baltus, Imhotep and Anck-su-namun.
Rick and Alex make it to the pyramid before sunrise, where the bracelet detaches from Alex's arm. Ardeth regroups with the Medjai in case Anubis's army rises. Evelyn is mortally stabbed by Anck-su-namun. Baltus puts the bracelet on and revives the Army of Anubis. Imhotep's powers are taken by Anubis, forcing him to fight as a mortal. Rick finds Imhotep summoning the Scorpion King and fights him, but the Scorpion King interrupts them, and Imhotep claims that Rick intends to kill him. The Medjai battle Anubis's army of jackal warriors. While Rick and the Scorpion King fight, Baltus is killed. Jonathan and Alex steal the Book of the Dead from Anck-su-namun and use it to resurrect Evelyn, who confronts Anck-su-namun while Alex and Jonathan help Rick.
The scepter Jonathan has been carrying extends into a spear that can kill the Scorpion King. The Medjai defeat Anubis' army, but find they have only defeated the vanguard. Rick sends the Scorpion King and his army back to the Underworld by killing the Scorpion King with the spear of Osiris, causing the oasis to be sucked back into the pyramid. Rick and Imhotep hang above a pit that leads to the underworld. Evelyn risks her own life to save Rick, but Anck-su-namun abandons Imhotep, who chooses to fall to his death. Anck-su-namun falls into a pit of scarab beetles and is eaten alive. The O'Connells reach the top of the sinking pyramid, and Izzy arrives with a modified dirigible and rescues the O'Connells as the oasis and the pyramid disappear. They depart into the sunset.
- Peter Griffin, Glenn Quagmire, Cleveland Brown, Joe Swanson, The Crystal Prep Girls, Blythe Baxter, Zoe Trent, Pepper Clark, Penny Ling, Vinnie Terrio, Sunil Nevla, Minka Mark, and Russell Ferguson guest star in this film.
- Ernie the Giant Chicken and The Dazzlings will work for Imhotep in this film.
- The storyline concludes in Ed, Edd, n Eddy vs. The Mummy: Tomb of the Dragon Emperor.