In ancient Egypt, Imhotep engages in an affair with Pharaoh Seti's mistress. When they are caught, Imhotep is mummified alive, cursed to become immortal. In 1923, Rick O'Connell and Evelyn Carnahan lead an expedition to find the lost city of Hamunaptra, where Imhotep is buried. They accidentally awaken Imhotep, who seeks to resurrect his lost love. As they face plagues and battles, they must find a way to stop Imhotep before he brings destruction upon the Earth.

In 3067 BC, the Scorpion King and his army are defeated and exiled to the desert. In 1933, Rick and Evelyn O'Connell explore an Egyptian pyramid and discover a Bracelet of Anubis. Their son Alex wears the bracelet and is captured by an Egyptian cult who resurrects Imhotep to defeat the Scorpion King. The O'Connells set out to rescue Alex, facing mummified pygmies and battling the cultists. Imhotep's powers are stripped by Anubis and he fights the Scorpion King as a mortal. Rick kills the Scorpion King and defeats the Army of Anubis. Imhotep and Anck-su-namun die.

In the Far East, Alex O'Connell unearths the mummy of the first Emperor of Qin, a shape-shifting entity cursed by a witch centuries ago. In ancient China, the Emperor becomes The Dragon Emperor, unites the country's kingdoms, and orders the construction of the Great Wall of China. Years later, Alex locates the Emperor's tomb with the financial backing of archaeology professor Roger Wilson. They revive the Emperor, who plans to raise his undead army and conquer the world. Along with the O'Connells and Lin, the group battles the Emperor and his Terracotta Army to save the world. Alex and Lin fall in love, and ultimately defeat the Emperor.