Desperate to find a way to stop Apophis, Carter and Sadie began searching for another way than their last resort plan: an execration that probably wouldn't work and would likely cost them their lives. After learning that the copies of the Book of Overcoming Apophis written by the evil magician Setne are being destroyed, Carter and Sadie lead a team to the Dallas Museum in an attempt to save the last copy. While there, Setne appears to Sadie who has no idea who he is and tells her that she can't save the scroll but to save King Tut's shadow box instead, that it will give her a clue. They fail to save the scroll and only drive off Apophis by Sadie invoking Ma'at, which nearly kills her. After learning that the box contains King Tut's sheut, or shadow, Carter comes up with the idea that if they capture Apophis' sheut and they execrate that instead, they might be able to destroy him. Anubis confirms this when he visits Sadie at her school dance, telling her that the sheut is like a "back-up copy" of the soul and that if it is destroyed, the being it belongs to will be destroyed as well even if they are a god. He also confirms that Apophis has a shadow which is sucking in the souls of the dead including Ruby Kane for more power. Carter and Walt Stone visit the god of knowledge Thoth for information on how to actually perform the spell, but while he confirms that the spell, which he calls a shadow execration is their best hope, he refuses to reveal how to find Apophis' shadow or perform the spell, but instead directs them to Setne who created such a spell and the Book of Thoth that he had stolen that contains the locations of all the gods shadows. However, he warns them that they need to do it before sunset because Setne is going to be on trial for his crimes in the Underworld and will be destroyed.
Carter and Walt travel to the Land of the Dead on the Egyptian Queen, meeting up with Sadie and Zia Rashid at Sunny Acres where they have been visiting Bes as Sadie has come up with a plan to use Bes' shadow to restore his ren which he lost to the moon god Khonsu. Arriving at the Land of the Dead, Walt uses the knowledge he has gained from Anubis to get past one of his jackal guards into the Hall of Judgement where they tell Julius Kane/Osiris everything that they have learned and have planned. Julius is furious at first, but agrees to support them before the trial of Setne begins. When Setne is about to be sentenced to destruction, he reveals that Carter and Sadie need him and they explain to Julius the fact that he holds the key to destroying Apophis. Unwilling to believe Setne but convinced to at least hear him out, Julius has Setne hold the Feather of Truth as he tells them that he has come up with a way to capture a shadow and destroy it and that it can be used to destroy Apophis. Setne then explains that it is very complicated and that they will need his help to do it. The Feather proves he is telling the truth and he reveals to Sadie that her plan to revive Bes should work and tells her that she and Walt should go and enact it using information he gives them while he, Carter and Zia retrieve the Book of Thoth and get Apophis' shadow with everyone meeting up afterwards. Setne also promises not to try to escape or kill them at least until they get the shadow. With no other choice, Julius agrees and Setne is released into Carter's custody controlled by the Seven Ribbons of Hathor.
Attack by the Demonic Hippo
Carter, Zia and Setne take the Egyptian Queen to the surface and Setne directs them to the ruins of Memphis, though he refuses to specify more until they get closer out of fear that Apophis will learn where they are going. After enduring taunting by Setne, Zia takes him to tell the ship's demon captain Bloodstained Blade where to go and Set appears to explain to Carter that he isn't controlling his uncle Amos Kane like Carter fears, that Amos is summoning him for help and that Set is on their side in this matter. Set also warns them of an upcoming attack and after he disappears, a demonic hippo working for Apophis attacks. The hippo attacks the Egyptian Queen, damaging it and sends Zia into the water when she tries to hurt it with a column of fire. Setne offers Carter advice, but he refuses it and ties him up. Needing to give Zia time to get to safety and the Egyptian Queen time to get out of the way, Carter jumps on the hippo's head and stabbed the hippo in the ear with his khopesh. Unfortunately, this only had the effect of making the hippo angry and he loses his sword. The hippo tosses Carter off and he turns into a falcon and tries to claw out the hippo's eyes to no effect and he is forced to fly to safety. Again ignoring Setne's offer of help, Carter transforms back into a human and summons his combat avatar, but even in that, he is no match for the hippo and it bites into him. Desperate, Carter asks Setne for his help and Setne has him use a spell that translates into "Hapi, arise and attack." This causes the hippo to let Carter go and snap at the hieroglyphs he summoned. Carter loses his avatar while the hippo swallows the hieroglyphs. However, they summon Hapi, the god of the Nile and he flings the hippo into a limestone cliff, causing boulders to collapse upon it, killing it. Carter ends up on Hapi's head and gets him to bring the Egyptian Queen and Zia safely to shore. Hapi offers to help them get to their destination so Setne tells him its the serapeum, the temple of the Apis Bull and Hapi agrees to transport the three and the Egyptian Queen there. Hapi warns them that it is a trap and uses what he calls "Hapi pills" to transform them into water which then seeps inland to the temple where they return to human form.
Upon arrival, Carter orders Bloodstained Blade to fix the ship while he, Zia and Setne travel through the serapeum in search of the Book of Thoth. Along the way, Setne explains the history of the Apis Bull and the serapeum which he'd built himself. Coming across various traps, Setne disables them or directs Carter in how to disable them when he can't do it himself. Eventually they reach the Shrine of Apis where Setne has to cast a disenchantment in order for them to get in. They then have to wait as Setne talks with them about his and Carter's fathers, revealing that he is a distant relative of Carter on his mother's side. Finally, Setne reveals that they have to wait for the Apis Bull statue in the chamber to come to life so he can get to the Book of Thoth which is in the dais on which the Bull is sitting. The Bull wakes up and chases Carter and Zia and Setne refuses to help, saying that they need to distract it while he gets the Book of Thoth, which he claims only he can get due to the various curses protecting it. Carter and Zia run until they reach a circular chamber with four sarcophagi in it and daylight coming through a shaft in the ceiling. Carter tries to talk to the Bull when it arrives as it is connected to Osiris, but he fails and it attacks with fire, but Zia protects him. Zia tries to destroy the Bull with fire, but it has no effect on him. The Bull then fires a blast of heat at them which they dodge. When the Bull turns on Zia, Carter calls on Horus' strength and used a piece of coffin lid to attack the Bull. Even with Horus' strength, Carter has a hard time against the Bull and is blasted backwards and defeated by another heat blast. Zia catches the Bull's attention and channels Khepri's power to shield herself from another blast and fires a comet of fire at the Bull, destroying it. Zia nearly burns herself up before Carter breaks through to her and she passes out before dumps water on her to cool her down. Carter carries Zia out, meeting up with Setne who leads him back to the Egyptian Queen.
Bloodstained Blade's attack
Returning to the Egyptian Queen, Carter gives Setne permission to give Bloodstained Blade orders while he treats Zia. Setne orders Bloodstained Blade to take them to the Land of Demons where Apophis' shadow is then to kill Carter and Zia. Bloodstained Blade takes the ship into the Duat, setting course for the Land of Demons then happily heads off to kill Carter and Zia as he hates the Kanes. When Bloodstained Blade refuses to back down, Carter blasts him through a wall with the strike hieroglyph and puts up a shield to protect Zia while he battles the demon. Carter then runs, drawing Bloodstained Blade away from Zia and trying to escape him. Realizing that no one is steering the ship which is out of control, Carter heads for the wheelhouse but Bloodstained Blade tries to slice him across the stomach with his blade head, only succeeding in grazing the skin and impaling his blade head in the wall. As the ship is heading towards a waterfall, Carter points it at the shore and lashes the wheel in place, but is then kicked through a window by Bloodstained Blade, breaking some of his ribs. Desperate and unable to summon his khopesh back for some reason, Carter asks Horus to send him a weapon, but due to the god's powerlessness in that part of the Duat, all he gets is an ostrich feather. Trying again, Carter surprisingly ends with the crook and flail of Ra which are supposed to be with Ra. Spotting Setne trying to escape the ship which is about to crash into the Land of Demons, Carter binds him up again in the Ribbons and he falls into the River of Night. Bloodstained Blade gets the upper hand on Carter, but before he can kill him, Zia recovers and incinerates Bloodstained Blade. The Egyptian Queen, completely out of control, crashes into the shore and is destroyed. Carter and Zia are thrown into the air and Zia turns an amulet into a giant vulture that is able to slow their fall. On shore and relatively safe, Zia treats Carter's injuries with Nefertum's Balm and they have a picnic on the beach, even kissing before they continue on.
Capturing the Shadow
Carter and Zia pull Setne from the River and unbind him only enough to get the Book from him. Zia finds out that the shadow of Apophis is indeed in the Land of Demons, but is unable to read the map to its location. Realizing that Setne probably can, they unbind him and he reveals that not only can he guide them to the shadow, he can keep them safe from the demons inhabiting the land by casting a glamour on them that makes them look like demons. Setne claims that he only ordered Bloodstained Blade to kill them as it was the only way that he would've taken them to the Land of Demons and Setne claims that he expected them to prevail. With no other choice, Carter and Zia allow Setne to cast a glamour on them and guide them through the Land of Demons to the Sea of Chaos where Apophis' shadow is. Along the way, they pass through the confusing land which is always changing around them, passing the spot where in a vision Apophis sent Carter his mother was trying to resist the pull of the shadow. Along the way, they are protected from Chaos' influence by the Khepri beetle that Zia wears as a necklace. Finally, they reach the edge of the sea where they find an obelisk on a jetty that is apparently the first land that rose from Chaos. Approaching the obelisk, Zia is shocked to discover that the spell needed to summon Apophis' shadow is a simple summoning spell and not incredibly complicated like Setne made it sound. Setne explains that it is complicated for him because as a ghost he can't cast the spell. Zia casts the spell and summons the shadow, but Setne then betrays her and Carter, turning the glamour into bindings and taking the Book of Thoth from them. He then explains his plan to use the shadow to blackmail Apophis into being his slave, but before he can do anymore, Sadie arrives through a portal and binds up Setne, releasing her brother and Zia. Using the spell taught to her by Walt, Sadie is able to bind the shadow to a shabti, capturing it and they head off to try to find a way back to the mortal world, dragging Setne with them.
However, before Apophis' shadow was captured, it sent out a distress signal and an army of thousands of demons responds. Unable to open a portal back to the surface and with no other way out, it looks like the end for Sadie, Carter and Zia, but an army of senile gods from the House of Rest arrive led by Tawaret and a restored Bes having been summoned to help by Anubis. To the group's shock, they discover that Setne somehow escaped the Seven Ribbons of Hathor and escaped with the Book of Thoth though Carter and Sadie don't need it to perform the execration. The gods battle the army while Bes drives the three back to the River of Night in his new limo despite Carter's protests that they no longer have a boat with the Egyptian Queen destroyed. Upon reaching the beach, they are stunned to find as Bes expected Ra approaching with Sobek on the sun boat on his nightly journey. Ra picks them up and they join him on the rest of his nightly journey.
Return to the mortal world
As they travel back to the mortal world, Zia allows Ra to take her as a host and he is finally reborn. It makes it awkward for Carter due to his feelings for Zia, but Sadie gives him advice to not let it bother him. At sunrise, the sun boat emerges in the mortal world in the First Nome in Egypt to find it under attack by Apophis and the rebels. Ra gives command of the gods to Carter, explaining that he returned to fight Apophis not to resume his throne and heads off with Sobek and Bes to join Bast in battling the serpent while Carter and Sadie go to help their friends in the First Nome. Carter and Sadie merge with Horus and Isis once more and head off to help their friends before they deal with Apophis.
Carter and Sadie, joined by Walt/Anubis join the battle against the rebel magicians and help to finally defeat them. Then Carter, as the Pharaoh of the House of Life and leader of the gods leads the magicians and many gods into battle against Apophis. Using the captured shadow and the shadow execration spell, Carter and Sadie, using both their power and Horus and Isis' are able to finally destroy Apophis bringing success to the quest.