Back on Earth, Eliza, Corwyn Marne, Pennerton and Finton have taken the Osirian sarcophagus, Merytra and Jala back to Marne's house in Napoli. Eliza apologises to Astarte Marne for the disruption to her household, but Astarte seems quite capable of handling the strange events that have taken place. Eliza notices that the Marnes' baby daughter, Lucita, is unwell, and Corwyn admits that Lucita is unlikely to survive to her first birthday; this may be why he showed such sympathy to Justine's sense of loss when she learned that the black tree had corrupted the futures of the Faction's children. Eliza and Corwyn join Pennerton and Finton in the cellar, where they're watching Merytra and Jala, having broken the Great Ape's legs to stop him from escaping. Eliza fears for Justine's life and intends to rescue her, and although Merytra refuses to discuss her god or his Ship with infidels, Eliza is prepared to resort to desperate measures to find out what she needs to know.
Upuat wonders why Justine boarded the Ship without invitation when she knew this meant surrendering her rights as a free citizen, and is amused by her lack of reverence and respect towards her intellectual superiors. However, she is overwhelmed when they enter the court itself; the Osirians are gods by humanity's standards, and their thoughts are more tangible than even Justine is prepared to handle. When the Lady Nut addresses the court, even Justine's telepathy can't stretch to translate the Osirian formal tongue. Nevertheless, the Osirians are still bound by tradition, particularly Anhor, who is appalled to see that Upuat's new slave isn't yet bound to the court. Anhor must break off chastising Upuat when the time comes to invite the Second Divine Shield, brother of Osiris, into the court. During the ritual of greeting and observance, Justine learns that the newcomer is Sutekh. But the ritual does not go as planned; instead of answering the call with a ritual knock on the door, Sutekh's followers simply blast them open. As the courtiers begin to panic and a roaring wind fills the chamber, Upuat admits to Justine that he has no idea what's going on, which is what makes it so interesting.
Eliza tries looking for signs of Justine in Corwyn's books of Egyptian legend; since the Osirians exist on a different timeline, the events of their future may be written in Earth's past. But the text of the books changes as she reads it, and only the history-proofed Eliza can tell that it's different. The Osirian court was supposed to be holding a wake following the mysterious disappearance of Osiris, but instead, the legends now say that the Ship was attacked and conquered by Sutekh. Eliza has no choice but to force Merytra to speak. Meanwhile, Corwyn has been sitting up with Astarte, watching over Lucita and fearing that Eliza is starting to suspect the truth. Eliza now calls Corwyn down to the cellar, where she reveals that the Mal'akh can indeed be harmed by conventional weapons; it's just that they heal so quickly that it's difficult to kill them in battle. But that also means that it's possible to torture them for days, and Eliza sets about doing so to Jala before Merytra's eyes...
Sutekh's personal retinue of Nephil Mal'akh bear their god into the court, where he demands that Lady Nut acknowledge his absolute authority in the absence of Osiris. Since Sutekh has broken protocol, Lady Nut refuses to address him in the formal tongue, but Upuat has now taken an interest and volunteers his slave to act as Nut's mouthpiece. Justine reluctantly does so, and for the purposes of this conversation, she becomes an avatar of the Lady Nut. Nut offers Sutekh one last chance to back down and accept his rightful place as the second divine shield, but Sutekh dismisses this offer and departs, vowing to take what he wants by force. Amused, Upuat decides to show Justine more of the Ship, which is connected to at least 6,000 different noospheres and draws its power from Ra, the living sun at the heart of the Osirian court (though in truth, it's far more complex than just being alive). Upuat takes Justine to Ra, and she sees that it's surrounded by platforms; these are the stations of the Eye, and when one of the divine shields connects to these stations, they can tap into directly into the power of Ra. Osiris and Sutekh were best at channelling this power, since they were bred especially for the task -- but now Osiris is gone, and it doesn't take a god to work out that Sutekh must be responsible. In Osiris' absence, it falls to Upuat or Khephri to defend Ra, but Upuat admits that he doesn't much feel like going up against Sutekh, and will happily abandon his post if that's what it takes to survive.
Merytra gives in and tells Eliza how to use the sarcophagus; right now it could deposit her anywhere in the Osirian court, but if she primes it with a sample of Justine's biodata, she can refocus its end on Justine herself. Telling the others to look for her in the legends if she doesn't return, Eliza uses one of Justine's red hairs to prime the sarcophagus and leaps into the tunnel -- tripping over her own feet when she emerges, to her embarrassment. Justine is wearing her robes of indenture (robes with a familiar-looking collar), but she refuses to let Eliza "rescue" her; it looks as if Sutekh is about to take over the Ship, and Justine must find a way to stop him. Eliza reluctantly returns to the tunnel, but finds it branching off in different direction -- and she is then confronted by Sutekh, who forces his way into her mind and is amused to learn that the last scions of Faction Paradox intend to do him harm. Sutekh casts the dazed and traumatized Eliza back to Earth, telling her that he left the Faction's children dying in their cradles and that her world will be the first to face his judgement. He then makes his move, drawing on the elemental forces of Time to attack the Ship; the storm clouds that Upuat noticed earlier are moving in from the outer desert, and doing quite a lot of damage. As the other courtiers mill about in panic, Sutekh confronts Upuat, the only other Osirian with the power to defend the Ship against his attack. Upuat, straining to resist Sutekh's mental attacks, warns Justine to run while she still can -- and once she's gone, Upuat surrenders, claiming that he just didn't want his slave to see him in pain. Sutekh contemptuously dismisses Upuat and sets off to seize control of Ra while the Ship begins to crumble under the onslaught of the storm.
Eliza awakens back on Earth, aware that she's only alive because Sutekh wanted someone to tell the world what was coming. She's also realised that he claimed to have left the Faction's children dying in their cradles -- cradles that were empty when she and Justine arrived. Corwyn knew how to open the door beneath Pompeii, as if he'd been there before, and he doesn't like to talk about his daughter's illness. Eliza thus confronts Corwyn, who confesses that he and his wife are unable to bear children of their own -- and thus adopted the one child that they found alive and whole beneath the black tree. But Lucita is not only physically ill; she sometimes disappears for hours or even days at a time, and so do the furnishings in her room and even Corwyn and Astarte's memories of her. Eliza warns Corwyn and Astarte that Lucita isn't just incomplete physically; she was removed from the remembrance tank before it had a chance to grow her a future.
Justine then emerges from the space-time tunnel, and is horrified to learn that the sarcophagus had been moved; the others thought that it would be too dangerous to leave it near the black tree, but that's exactly where Justine needs to go, and now she'll never get there in time to stop Sutekh from taking over the Ship. She explains that she needs to bond biomass from the tree to the stations of the Eye, a process that could in fact strengthen the biomass in question rather than harm it -- and Corwyn, Astarte and Eliza realise that Lucita could serve that purpose. When Justine learns the truth, she confirms that this process would not only save billions of lives but also give Lucita a future of her own, and Astarte reluctantly hands over her baby daughter and allows Justine to take her to the Ship.
Upset by the torture he's witnessed, Finton returns to the cellar to apologise to Merytra, but when he unthinkingly speaks Sutekh's name she lashes out at him in fury, referring to Sutekh as the Abomination. Finton thus learns that Merytra didn't intend to summon Sutekh at all; Sutekh is the pale destroyer who forced her to serve him against her will, and the dark god she loves is the one who freed her and the Canaan Mal'akh from Sutekh's thrall. Their interrupted crusade would have been in the dark god's name, to erase all trace of Sutekh's name from the history of Earth. Merytra leaps into the tunnel to destroy Sutekh the Abomination, and Eliza, who's lost track of who wants what, follows her in case Justine needs to be protected. They are separated upon reaching the Ship, but Merytra finds her dark god -- Upuat, who had all but forgotten that he once freed some of the Mal'akh in order to teach Sutekh a lesson. When he learns that Merytra loves him and is still fighting her crusade in his name, he decides to take her on as his new chamber slave, as she'll be even more amusing than Justine.
Eliza catches up with Justine and accompanies her to the station of the Eye. There, the voice of Nut speaks to them, and Justine requests a formal audience. Sutekh arrives, descending to the Station without need for a barge, but finds that Justine has entered into communion with Nut once again and that the Paradox scions are thus safe from harm. Through Justine, who has put the pieces together herself, Nut has learned that Sutekh dealt with Osiris by burying his body beneath the Faction's remembrance tanks in Pompeii. Osiris' biomass thus spread out through the earth, corrupting the tanks and altering the biodata of the black flowers growing in Pompeii; the Osirian seers were unable to locate him because his biomass is now spread amongst several life forms instead of concentrated in one. But this means that Sutekh isn't rid of Osiris after all; Lucita, a child of the corrupted remembrance tanks, contains a part of Osiris' biomass. Realising the danger he's in, Sutekh swallows his pride and promises to spare the Earth and restore Faction Paradox's lost bloodline -- but Justine and Nut both know better than to believe his lies, and Justine thus presents Lucita to the station of the eye, bonding the baby to Ra, strengthening the Ship's defences, and driving Sutekh out of the Ship in a blaze of light.
Eliza returns to Naples with Lucita, to find that Jala healed more quickly than expected and broke out of the cellar right in front of the terrified Astarte -- but fled without harming her. He may be a Mal'akh, but he's still a soldier, not a merciless killer. Finton, recalling an earlier conversation with Eliza, wonders whether the Mal'akh who survived the earlier events will now be on the defensive rather than the offensive. Lucita is still not physically well, but Corwyn and Astarte turn down Eliza's offer to supply her with more biodata; they're frightened that Lucita will turn into something other than human, and at least their daughter now has a future. Eliza asks the men to clear the anachronistic technology out of Pompeii and keep it safe; the Osirian court will deal with the black tree, and Justine will remain on the Ship to act as a liaison between the Osirian court and the Great Houses. Eliza moves the tunnel's threshold back to England and departs, telling the men to destroy the sarcophagus after she leaves.
Back on the Ship, as Anhor prepares to deal with matters of repair and reconstruction, the voice of Sutekh speaks to him, ordering him to deliver a message to the court. Sutekh may have failed to take the Ship, but now the court has seen his power, and they know that even they are not as untouchable as they once believed. Unrest is spreading, and one day Sutekh will strike again -- and he will not rest until the Great Houses and Faction Paradox have come to dust.