After Julius Kane released the gods from the Rosetta Stone, a discord appeared between the Kane family and the House of Life. This led to the Kanes illegally teaching the Path of the Gods to students at Brooklyn House, drawing them the ire of Michel Desjardins. This led to the Battle of Brooklyn House where forces led by Sarah Jacobi and Kwai attacked after Desjardins agreed to an attack under the influence of Vladimir Menshikov. Thanks to the return of Ra revitalizing the magicians, Jacobi and Kwai's forces were defeated and fled. However, Desjardins had died banishing Apophis and Amos Kane was now Chief Lector of the House of Life. This caused discord with many of the nomes with Jacobi and Kwai riling them up and forming a rebel faction that fought for control of the House of Life at the same time the House was at war with Apophis and his forces.
Over the next six months, the rebels grew stronger, recruiting many nomes and destroying others which they blamed on Apophis or the Kanes but never themselves. They also refused to acknowledge Amos as the leader of their enemies due to believing (rightly) that he was calling on the power of Set and instead broadcast their messages to Carter Kane, leader of the Twenty-First Nome. Battles were fought between the two factions, but the rebels had the upper hand, being more ruthless and having more followers. Eventually, with the help of Shu, a young Russian magician named Leonid reached out to the House of Life to warn them that the threat was worse than they thought: Jacobi and Kwai were working with Apophis, though the other rebel magicians had no idea of that fact. Leonid had learned by accident while secretly studying the Path of the Gods himself and also learned that the rebels planned to attack on the spring equinox at the same time Apophis would fully rise into the mortal world to distract the magicians and keep them out of the battle with Apophis. After learning of this, Carter ordered that the Twenty-First Nome help protect the First Nome as the magicians of the Twenty-First, followers of the Path of the Gods, were the only ones who really had any chance against the rebels.
After successfully getting Apophis' shadow, the Kanes, Ra (in the form of Zia Rashid), Sobek, and Bes arrive on Ra's sun boat to find the First Nome under attack by Apophis. However, Zia and Ra point out that the inside of the First Nome is under attack by the rebels and Ra tells Carter and Sadie to go help Amos defeat the rebels as there will nobody left to save if the House of Life falls. Ra also informs Carter that he is now the pharaoh of both the gods and the House of Life and Ra will hold off Apophis until Carter returns to fight and tells him to keep the crook and flail to use as his weapon. Carter agrees and merging with Horus once again, turns into a falcon to fly to battle while Sadie similarly merges with Isis and follows as a kite.
Arriving at the tunnel beneath the Great Sphinx, they find that it has been blasted open and following it, find obvious signs of battle such as damage from explosions and a badly injured, but alive, Leonid. After leaving Leonid with a Slow spell to try to keep him alive, they arrive at the battle where a shabti lion tries to attack Sadie, but she changes it back to normal with the Divine Word Fah given to her by Isis. They find that apparently the rebels attacking through the tunnels caught the House's defenders off-guard and Jacobi and her elite men got into the Hall of Ages to fight Amos alone while other rebels blocked the reinforcements from the House from getting through to him. Entering the battle, Sadie turns a magician fighting Julian into a hamster while Carter destroys a rhino conjured by another evil magician. They find that Felix is using an ice spell to turn magicians into snowmen and has his army of penguins attacking anyone who gets in his way while Alyssa fights another Earth elementalist who is no match for Alyssa who has the power of Geb behind her and is trapped up to her shoulders in quicksand by Alyssa. Cleo was being treated by Jaz after having her arm turned into a sunflower, but had turned her enemy into a human-size volume of the novel David Copperfield. Shelby had scattered her crayons to trip up enemy magicians and was whacking them with her wand. She also turned a metal warrior into a potbellied pig. Some of the residents of the First Nome were helping too by throwing talismans and deflecting spells. With all of this help, Carter and Sadie are able to reach the doors where Walt Stone, now merged with Anubis, single-handedly battles the guards on the doors. Walt is able to throw one magician with inhuman strength, encase another in mummy linen, disintegrate the staff of a third and then shrink down all the surviving rebels and trap them in canopic jars. After making sure everyone is alright, Walt uses his powers to turn the doors to the Hall of Ages to dust and the initiates charge inside to help Amos.
In the Hall of Ages, the initiates find the rebels, led by Sarah Jacobi and Kwai attacking Amos who is now hosting Set and using his combat avatar. Kwai attacks with bolts of lightning that do nothing while Jacobi uses netjeri blades that wear down the avatar. Other magicians attack with gusts of wind and water, shabti creatures and in one case, cheese to little effect. Set, with Amos struggling to control him, knocks Kwai flying and one man into the curtains of the Roman Age, stunning him and encases the cheese master in a sandstorm that Amos stops before it kills him. The Kanes and the initiates are stunned as it seems Set is controlling Amos again, but Sadie realizes that its really the other way around and Amos is controlling Set. After hesitating for a moment, the initiates charge into battle to help Amos, but noticing them, Jacobi orders the real attack to start, having simply been distracting and weakening Amos up to that point. On Jacobi's signal, Kwai blasts Amos in the face with lightning while the other magicians lasso him with ropes, weakening him . Jacobi then puts a noose of her own around Amos' neck, bringing him down and dissipating the avatar until Amos was only surrounded by the thinnest of red shields. Using this to her advantage, Jacobi puts one of her blades to Amos' throat and demands the initiates stop. While Sadie and Carter want to help Amos, Isis and Horus don't since Set is an old enemy and Horus even prevents Carter from forming a combat avatar, causing the Kanes to stop being the Eye of their respective gods due to the disagreement. Jacobi tries to use the situation to her advantage, telling everyone that the Path of the Gods has only brought confusion, Chaos and Set himself in the Hall of Ages. Set is infuriated by the fact that his attempt to help led to this and Sadie tells Jacobi that Amos is channeling Set's power and is in control and Set is a useful ally when properly managed. Amos tries to get Sadie to flee and go fight Apophis instead, but Sadie insists on fighting for Amos as their Chief Lector and uncle. Jacobi declares herself the new Chief Lector and sentences Carter and Sadie to death while offering the initiates amnesty if they surrender. Sadie points out that Jacobi is working with Apophis and in anger, Jacobi blasts her with ha-di. As Isis isn't helping anymore, the spell shatters Sadie's shields and flings her back into the curtain for the Age of the Gods, stunning her. When Carter tries to help, Kwai blasts him with lightning, stunning him too. While Jaz attempts to help Carter, the other initiates are stunned and Jacobi adds to this by using magic to tell them to give up. She then throws one of her blades at Sadie, but before it can kill her, Walt grabs it and turns it to dust. Jacobi's attempt on Sadie's life angers both Walt and Anubis and they open a chasm in the ground from which the spirits of the dead swarm, wrap Jacobi in ghostly linen and drag her to the Underworld, making Set proud of Anubis for his actions. Carter, relatively uninjured, takes the opportunity to try to get the rebels to see sense, telling them that Apophis is outside being held off by a few brave gods and they all need to go out and help them as Jacobi and Kwai led them astray. Sadie points out how the rebel attack was timed at the same time that Apophis was rising so the magicians would be fighting one another rather than him. Finally, the rebels listen and turn on Kwai, releasing Amos. However, Kwai channels Apophis' power, telling them that they're too late as Apophis is currently destroying the gods and will swallow the sun and everyone will die. Now on the same side, both the rebels and the initiates attack Kwai.
As the magicians turned on him, Kwai blasts everyone with his lightning. Isis, Anubis and Set protect Sadie, Amos and Walt respectively while Carter manages to deflect the blast aimed at him. However, everyone else is knocked out by the attack. As Sadie prepares a binding spell, Kwai conjures creatures to attack the defenseless magicians and Sadie focuses on protecting them at Amos' order. Amos attacks the creatures, but they just reform. When Carter tries to attack Kwai in his combat avatar, Kwai blasts him again and he is sent into a stone column which collapses on top of him, but his avatar protects him. Walt summons all of his magical animals to protect the fallen magicians and then turns to face off against Kwai himself who is unimpressed at being faced with Anubis. Walt summons jackals and battle armor with a was staff. Walt is able to deflect all of Kwai's attacks and his jackals attack Kwai, distracting him and allowing Walt to hit him with a massive blow from his staff. The blow defeats Kwai and his creatures vanish. However, Kwai refuses to give up and uses up all his life force to cast sahei or bring down causing him to turn to sand and the Hall of Ages to start to collapse. While Amos wants everyone to get out, most of the other magicians are still recovering from Kwai's attack and won't get out in time so Sadie asks if there's no way to save the Hall. Such a thing is beyond the powers of Set, Anubis and Horus so Sadie realizes its up to her and Isis. Sadie calls on Isis and then finds the calm in herself before casting Ma'at. Calling upon Ma'at restores order to the Hall and repairs it, saving everyone and ending the danger.
Using so much power causes Sadie to pass out for a moment, but she quickly recovers. By the time she wakes up again, the other magicians have recovered from the attack and Carter lets her know that they have to get to the surface and help finish Apophis even though they both know that they've used up too much energy in this battle and were in no condition to fight Apophis, though they had little choice. Amos offers Carter the throne of the pharaoh and asks him to lead the gods and magicians into battle. Though he secretly has doubts and fears, Carter accepts the role of pharaoh, though he tells them taking the throne will have to wait until after the battle and when Amos rallies the magicians, even the former rebels agree to fight under his command. Carter then uses his new position to gather reinforcements from the gods and leads both forces into battle against Apophis. Using the shadow execration, Carter and Sadie are able to destroy Apophis and Carter is made pharaoh. This also brings an end to the rebel faction as they reunite with their brethren in the House of Life.