At the Tomb of Alexander the Great, Arthur Harrow collects Ammit's ushabti from Marc Spector's dead body and leaves to complete the ritual. Mourning Spector's death, Layla El-Faouly disguises herself and follows Harrow and his followers. On their way to Giza, they get stopped by the Egyptian Patrol Agency, but Harrow uses his new powers to judge the patrol guards, killing the unworthy. El-Faouly prepares to attack Harrow, but Taweret stops her, sending her a message from Spector, saying that they need Khonshu's help to stop Harrow.
Harrow and his followers arrive at the Great Pyramid of Giza, making their way into the Chamber of the Gods, although the Ennead Council stands in their way. Despite their resistance, Harrow kills Selim, Yatzil, and other Avatars, before breaking the ushabti and releasing Ammit from her imprisonment. Ammit tells Harrow that his Scales are not balanced, and although he is ready to accept his destiny, Ammit delays Harrow's death and chooses him as her new Avatar. Meanwhile, El-Faouly frees Khonshu but refuses to become his Avatar, so he confronts Ammit by himself.
Spector finds himself in the Field of Reeds, where Taweret tells him that he is complete now and can achieve his peace. However, Spector refuses to stay in the paradise, while Steven Grant is trapped in the sand of Duat, and turns his back to the Field. Finding Grant frozen in the sand, Spector apologizes to him for failing to protect his peaceful life and places his full heart into Grant's hand, before freezing himself. At that moment, the Gates of Osiris open near them and the light liberates both Spector and Grant, so they can leave Duat. As Taweret helps them by slowing down the sandstorm, Spector and Grant successfully escape Duat.
Khonshu senses Spector and Grant's presense in the world of living and makes a new deal, healing their body and bringing Moon Knight back to life. Spector and Grant ask to redefine their arrangement, saying that after Ammit is no longer a threat, they are free to go. Khonshu is appalled that they would negotiate now but has no choice but to accept their terms. Meanwhile, El-Faouly gets told by Selim, that the only way to stop Ammit is to imprison her inside the vulnerable human body, instead of ushabti. Without any other options, El-Faouly speaks to Taweret and accepts her offer to become a temporary Avatar, and Taweret grants her with the ceremonial armor.
Harrow unleashes his newly-granted forces on Cairo, while his followers judge people, sending the souls of the unworthy to be devoured by Ammit. However, he gets confronted by Moon Knight (and Mr. Knight, as well), while Khonshu battles colossal Ammit. She once again offers Khonshu to join her, but Khonshu says that he punishes only those who had chosen evil and gives them the choice, while Ammit only takes it away. Joined by El-Faouly, Spector and Grant continue to fight Harrow and his disciple, but they fail, while Khonshu gets defeated by Ammit. Suddenly, Spector blacks out and finds Harrow being brutally beaten and other followers dead, realizing that nor he, nor Grant did it.
Spector and El-Faouly then bring Harrow to the Chamber of the Gods and recite an ancient spell to trap Ammit inside Harrow's body. Khonshu orders Spector to kill Harrow, so both of them would no longer be a threat, but Spector refuses, saying that Khonshu is barely different from Ammit. Upholding his part of a deal, Khonshu releases Spector and Grant, as they find themselves at the Putnam Psychiatric Hospital with Duat's Harrow. Although Harrow refuses to admit that what they said was true, but Spector and Grant notice blood on Harrow's footprints, saying that he does not know as much as he thinks. Spector and Grant dismiss Harrow's diagnosis and choose to save the world, waking up in Grant's apartment in London.
In the mid-credit scene, Harrow is seen to be administrated to Sienkiewicz Psychiatric Hospital, where he gets taken out by a Spanish-speaking man. Noticing dead hospital employees on their way, Harrow is taken into a limo, where he meets Khonshu, reminding that he cannot hurt him or Ammit. Khonshu tells Harrow that he had no intentions of taking El-Faouly as his next Avatar and Spector does not even know how broken he truly is. Khonshu then presents Harrow with Jake Lockley, another alter of Spector, who shoots Harrow and drives away.