The story starts with the crystal Orb of Nabu shining across the world, something Doctor Fate says "portends the struggle I have dreaded all my life!"
The orb directs Fate to the Boston Museum of Egyptology where he finds the recently broken bodies of two men and then is confronted by a mummy embodied by the spirit of Khalis, a servant of Anubis. Regardless of the fear Doctor Fate professed earlier, here he exclaims "...you flatter yourself, evil one, if you think Doctor Fate might fear one such as you!"
Unfortunately for Fate, Khalis is siphoning the power from the Doctor, using it to power himself. Khalis says that his power comes from the amulet that Fate wears, the Amulet of Nabu, which he steals and runs away with.
Doctor Fate calls upon Ka, the Lord of the Ethereal Plane to join his mind with that of Khalis but is too weak. Fate returns back to his tower and enlists Inza's help to heal his human wounds. While tending to Kent, she complains about being nothing more than a nurse to Doctor Fate's human face and how her husband is not Doctor Fate. She says she is a prisoner in the tower.
Kent spends countless hours pouring over scrolls and books looking for references to Khalis. In 2030 BC, on the river Nile, a mad priest named Khalis spread the word of coming deaths at the hands of the god Anubis. As a reward for his devotion, Khalis was given the Amulet of Anubis.
Khalis used the amulet to enslave legions to build temples for Anubis until confronted by the human form of Nabu. Defeated, Khalis is set upon by the now-freed slaves who mummify and entomb him. Anubis curses Khalis with "life-in-death" until he has recovered the stolen amulet.
Doctor Fate now knows that the Amulet of Nabu is really the Amulet of Anubis.
Away from the action, Inza feels guilty for her early rant and decides to go to the museum to see if she can dig up some clues about Khalis. Doctor Fate finds Khalis and fights him with his fists while conserving his mystical energies for a single blow. During the fight he calls upon Tezcatlipoca, the god of trickery, for help disorienting Khalis. In one strike, Doctor Fate summons the light from all of Boston and directs it against Khalis who is not destroyed but escapes in defeat.
Inza finds a tablet that contains Khalis's magical name and also apologizes for her earlier anti-Fate rant. In response, the Doctor replies "You've been a great help, Mrs. Nelson!"
After returning the light to Boston's night, the city is found transformed by the addition of a sphinx and a pyramid. Awakened by Khalis's pleas, Anubis is angry and threatens Khalis for his petulance. Anubis taunts Khalis by saying that he might consider his cause if he destroys Doctor Fate.
Using the seal that Inza found, Fate speaks the spell written on it which summons Amon-Ra the sun god to help destroy Khalis, who crumbles to dust. The spell was "hetepkheti tefnakhte! Amon-Ra menteptah!"
Inza finds Doctor Fate on the side of the road, spent and wounded. He says ""we did it...we: you and me" to which Inza responds "AND Dr. Fate".