The Battle of the First Nome was the final battle in the War Against Apophis.
Following the rise of Apophis, the Kanes and their allies in the House of Life work on finding a way to defeat them. Eventually, with the help of the ghost Setne, they come upon the idea of a shadow execration, a spell that destroys Apophis' shadow or sheut to destroy him. Carter, Zia and Sadie embark upon a quest for the shadow with the help of Setne and get it, though Setne escapes with the Book of Thoth.
After getting Apophis' sheut and Zia becoming the host of Ra, Carter, Sadie, Ra, Bes and Sobek arrive in Egypt to find that Bast is single-handedly fighting Apophis who has risen. Ra takes Bes and Sobek into battle with him while instructing Carter and Sadie to help their friends defeat the rebels who are attacking the First Nome. He also tells Carter that he, as the Eye of Horus is now the Pharaoh and he had only come back to fight Apophis. Once the rebels are defeated, Carter is to gather the gods under his leadership to fight Apophis.
After defeating Sarah Jacobi and Kwai, the rebels and the House of Life unite once more and agree to fight Apophis together with the House now accepting Carter as their Pharaoh and leader. Emerging from inside the First Nome, they find the four gods continuing their battle against Apophis, but with only Ra having any luck in hurting the Serpent who keeps growing stronger while the gods are getting weaker. Carter orders the others to wait for his signal then sends his ba to the throne room of the gods where dozens show up when he calls them including Serqet, Khonsu, Nekhbet, Babi, Shu, Nut, Hapi and Neith. Despite having hoped for more of the gods friendly to them, Carter realizes that they are unable to come and more are under attack by the forces of Chaos and decides to make due with what he has. Carter informs the gods that Ra made him their leader and asks them to follow him into battle. When Serqet challenges him, saying they only follow the strong, Carter hits her with his flail, briefly turning her into a pile of burned scorpions. The gods then accept him as their leader and charge into battle. Once he returns to his body and sees the gods arrive, Carter orders his fellow magicians into battle.
Despite the amount of fighters they have, Apophis is able to separate them all by splintering the Duat into many layers so that the gods and magicians are each fighting a form made up of a fragment of his power. Walt Stone ends up trapped with Apophis coiling around him. Walt tries to get out by blasting Apophis' scales to ashes, but they just regenerate and Apophis' draws closer and closer to him. Julian summons a full Horus combat avatar and slashes at one version of Apophis' tail while the tail tries to impale him. Serqet also faces a version of Apophis' tail, using her own scorpion tail to effectively sword-fight it. Amos faces off with apparently nothing, slashing his staff and shouting command words. However, while Apophis splinters his form to fight them, fighting so many beings at once doesn't seem to weaken him at all. Carter and Sadie realize that Apophis is working to separate them and use Ra's crook to stay together, trying to reach Ra to help him. Apophis tries to crush them with one of his coils, but Carter destroys it with a strike from the flail. As they continue, they spot Babi riding one version of Apophis' head and slamming it with his fists, but doing nothing more than mildly annoying him. At the same time, Neith shoots arrows at another head of Apophis to no effect and yet another bites Nekhbet, destroying her. Finally, the two reach Apophis' true head which is battling Ra. While Ra is able to burn Apophis' skin and eyes, the injuries heal almost instantly and he keeps growing stronger while Ra grows weaker. Bast also attacks Apophis' real head with her knives, but Apophis simply shakes her off each time. The two find Bes who Apophis had thrown to the ground and trapped under a massive block of limestone. Carter uses the strength of Horus to shatter the block and free Bes, but breaks a few bones in his hand in the process. They then head to help Ra and Zia who inform them that Apophis is getting stronger. Unfortunately, their appearance distracts them and Apophis is able to swallow Ra. Enraged, Carter attacks Apophis with the crook and flail, inflicting three massive gashes across his neck that don't close, but Apophis isn't affected by the injuries at all. With Ra gone, the sun disappears in the sky, the temperature drops and cracks spread across the land. The swallowing of Ra causes all the gods and magicians to lose hope except Bes and Bast who try to rally Carter and Sadie who are deep in despair. Apophis gloats in triumph and offers the Kanes their lives if they surrender. Carter initially considers it, but after seeing the glow of Ra continuing down Apophis' throat and remembering how he and Zia had sacrificed themselves for the world, Carter decides not to give up and has Sadie pull out Apophis' sheut.
Carter and Sadie prepare to cast the shadow execration and despite having a bit of fear, Apophis tells them the spell won't work now that he's at his strongest after having swallowed Ra and threatens to raise their spirits and their parents' from Chaos again and again if they try to torture them for eternity. The threat enrages Carter who merges with Horus again and becomes more determined than ever to destroy Apophis despite knowing that he and Sadie are so low on energy that even with the help of Horus and Isis, they will likely burn up. Carter throws the crook and flail into Apophis' face, blasting him with a column of fire and he and Sadie prepare to cast the spell. Needing to buy time to perform the spell, Carter asks Bes and Bast to keep Apophis busy and both agree and attack Apophis as the Kanes begin the shadow execration. Bast ends up being thrown into a stone block, causing Bes to hit Apophis with a club so hard his eyes rattle in his head. Apophis attempts to bite Bes, but Bes hangs onto one of his fangs as he tries to shake him off. During the fight, the Kanes perform the spell despite Carter's fears due to the fact that execrating just a partial manifestation of Apophis cost Michel Desjardins his life. Horus and Isis also protect Carter and Sadie from the effects of Apophis' power as they perform the execration. As they reach the naming of the enemy part of the spell, Carter finally understands why destroying Apophis' sheut will destroy him: a being's shadow is more than just a back-up copy of their soul, it stands for their legacy, their impact on the world. With no shadow, a person's existence becomes meaningless and they can't be alive. Carter realizes that even if Apophis survives the execration, destroying his shadow will cut his connection to the mortal world and he will never be able to rise again. Apophis eventually manages to dislodge Bes and send him flying into the side of the Great Pyramid, but the Kanes have reached the end of the spell at that point and recite the last lines before he can react. The shadow is destroyed, releasing an explosive wave of darkness that knocks the Kanes off their feet. The destruction of Apophis' shadow shatters his legacy upon the world and causes all of the wars, murders, turmoil and anarchy Apophis has caused since ancient times to lose their power and finally stop casting their shadow across the world's future. The destruction of Apophis' shadow also releases the thousands of ghosts it had consumed for power, including Ruby Kane and they return to their rightful places in the afterlife. With his shadow destroyed, the world returns to normal and Apophis begins to shrink, warning them that they haven't just killed him but have also exiled the gods who have disappeared. As his scales fall off in smoking pieces, Apophis gloats that Ma'at and Chaos are linked and to push him away also pushes away the gods. As Apophis tells them that Ra shall die within him, his head explodes and Ra and Zia emerge from his body. Apophis crumbles into sand and steaming goo, destroyed.
Zia collapses, exhausted and the return of Ra causes the sun to return, the temperature returns to normal and the cracks in the ground to repair themselves. Ra informs them that Apophis was right and that the gods must now distance themselves from the Earth for a time now that Apophis is gone. Ra asks Carter to take care of Zia and tells him to keep the crook and flail as he is the rightful Pharaoh. Ra then leaves and Horus and Isis disappear from Carter and Sadie's minds. With Apophis destroyed, the House of Life is united once more and Carter is officially made the Pharaoh. He chooses, however, to leave the day to day running in the hands of the Chief Lector Amos Kane while he runs Brooklyn House and lives a normal life. Carter and Sadie visit their parents who aren't angry about the escape of Setne though he has the potential to pose a great threat with the Book of Thoth and inform them that due to the gods leaving, they won't be seeing much of each other anymore for awhile. Ruby Kane informs Sadie that Anubis is allowed to stay on Earth, however, as he has taken Walt as his permanent host and will be able to live a mortal life, something he has never had before. They later visit the House of Rest to say goodbye to Bast and Bes who show them that Horus has officially become the Pharaoh of the Gods once more and Bes offers to still help them if they need it, saying that its always been easier for him to cross the Duat than the other gods.