Princess Ahmanet was ready to succeed her father as ruler of Egypt until his wife gave birth to a baby boy. Knowing the child would take her place, Ahmanet sold her soul to Set, god of death, and murdered the Pharaoh and his family before attempting to sacrifice her lover to give Set a body of his own. She was stopped and mummified alive to prevent her evil from spreading.
In the present day, mercenary Nick Morton (Tom Cruise) uncovers Ahmanet's tomb and accidentally brings her back to life. Ahmanet (Sofia Boutella) tries to use Nick as the new host for Set while also regenerating her own body to unleash her wrath upon the world.
Ahmanet is at one point captured by agents of a corporation called Prodigium, led by Dr. Henry Jekyll (Russell Crowe), which is dedicated to protecting the world from supernatural forces. Ahmanet possesses an agent to break her free and let her get a magic dagger from Set that she intends to use on Nick.
Nick ultimately takes the dagger and stabs himself with it to be possessed by Set and battle Ahmanet. He defeats her by sucking the life out of her. Prodigium takes Ahmanet's body and fills her sarcophagus with mercury to hold her evil spirit down.
Nick now roams the desert as a half-man/half-monster hybrid, with Jekyll holding out hope that Nick can be saved.