300 years later, two Englishmen named Pennerton and Finton, representatives of the Society of Sigismondo di Rimini, arrive in the Italian village of Posto di Ferragio to observe a curiosity in the possession of the town’s mayor: a grotesque giant ape that shuns the daylight and is unlike anything either of the Englishmen have ever seen. The mayor, Don Escuro, hopes that the Englishmen will recommend his discovery to their secret society, putting his village on the map; thus, he keeps quiet about the recent discovery of bodies that have been savaged and drained of blood. Also, a foreign woman, Merytra Ellainya, has been showing up uninvited at the animal’s cage, almost as if she’s speaking to it. Don Escuro angrily sends her on her way, but notes that, like the grotesque, she keeps her face covered in the sunlight.
Pennerton and Finton return to Naples, shaken by the sight of the monster and fearing that their Society’s dabblings in esoteric matters of ritual and science may be responsible for letting the beast into the world. Finton reveals that his friend, the Earl of Sandwich, has told him of bizarre events that recently took place in London; a group known as Faction Paradox was involved, and if it’s true that the Mal’akh are returning to Earth, then perhaps the Society should seek an alliance with this Faction. Another member of the Society, Corwyn Marne, overhears their conversation and reveals that he’s heard of Faction Paradox before; apparently, it’s one of many forces engaged in a battle to control history, just as the great houses of Europe and the Near East have been fighting over control of the Mediterranean through the many cultures that have grown up around it. Pennerton scoffs at this bizarre claim, but Marne nevertheless proposes that the three of them meet at his home the next day to summon Faction Paradox and request their help in the matter of the Great Ape.
Back in Posto di Ferragio, Don Escuro learns that his creature has been stolen and that Merytra has been seen in the village square. Escuro storms off to confront the foreign woman, angrily telling her that, in a Christian village, she is considered no better than an animal. But the amused Merytra then calls forth the “ape,” whom she refers to by name as Jala. To Escuro’s horror, the square is full of the monsters, who have been closing in for some time; since Jala is the least able to avoid notice, they decided to let him stay in captivity while the others remained in the shadows, hunting and gathering strength. Now they are all here, and Jala holds the terrified Escuro prisoner while the rest of the Mal’akh move out into the town to make their presence known.
The next morning, Pennerton and Finton arrive at Marne’s house to summon the agents of Faction Paradox. Mrs Marne -- who seems to know at least as much about the Faction as her husband -- leaves the men to conduct the ritual, which consists of sacrificing political pamphlets to the fire, creating a trail of propaganda that rewrites the mood of the country and points across Italy to Naples. To Pennerton and Finton’s surprise, a young woman named Justine then walks into the study, claiming to have come in answer to the summons. Shaken, Pennerton explains that their Society was founded to keep watch on the Mal’akh, and he fears that the Great Ape in Posto di Ferragio is a sign that the corruption is returning. Justine takes little interest until Marne claims to know that Faction Paradox is on the verge of extinction; however, when the Faction made contact with human history in 1752, they left behind certain artefacts, such as race banks and biodata codices, which Justine could use to create a new Faction outpost. Marne has worked out the location of the relics, which he will give to Justine in exchange for her help. Justine agrees to the bargain and contacts her partner, Cousin Eliza, who has been asking around and has heard rumours of the deaths near Posto di Ferragio -- and legends that the Mal’akh were drawn out of hiding in the 15th century by a dark and powerful god.
In Posto di Ferragio, Merytra and her Mal’akh servants place an Egyptian sarcophagus in the town square; there is no longer anyone about to stop them, save Don Escuro, who is too busy begging for mercy. As night falls, Merytra addresses the Mal’akh hordes, reminding them of how they were betrayed; they could have been all-powerful, but their god was taken from them, their children were burned to dust, and the bright future they had been promised was stolen away from them. Now, Merytra intends to bring the Mal’akh god back to Earth, but before she can begin the ritual, Justine steps out of hiding and confronts her, recognising the sarcophagus as the lodestone of a time-space tunnel. Marne, Pennerton and Finton watch from hiding as Justine and Eliza take on the assembled Mal’akh hordes, who are unused to fighting after centuries of hiding in the shadows; now those shadows turn on them as Justine and Eliza unleash their Faction shadow weaponry. Frustrated, Merytra retreats to the mayor’s house to fetch the real sacrifice -- not Don Escuro, who was only meant to serve as a snack for her forces. Justine strikes down Jala and pursues Merytra to the house, where she finds Merytra clutching a bizarre animal like nothing on Earth. Merytra insists that Faction Paradox has no right to interfere, as they no longer have any stake in this world; in her words, “the tree is barren.” Justine recognises the animal as something with history in its veins, and, horrified, she despatches it with a swing of her shadow sword. She then demands to know the nature of Merytra’s dark god, and exactly where Merytra found her intended sacrifice.
Merytra tells Justine of her experiences on the dark god’s homeworld. There, she once watched, under the thrall of the god of destruction, as he spoke with another of his kind, Upuat. The Destroyer had summoned the Mal’akh to Earth in order to incite violence in a critical period of history and force the Great Houses to make a truce with his people. However, his subtle achievements were overlooked in favour of his brother, Osiris, who had led public and violent campaigns against his people’s enemies -- and the bitter god of destruction vowed to challenge Osiris, take his rightful place as captain of the Ship of a Billion Years, and lead his own victory parade through a world brought to dust.
Marne and his friends arrive at the house as Merytra speaks, and the distraction enables Merytra to get past Justine; however, Justine lets her go, claiming that she is powerless now that she’s lost her sacrifice. She demands to know where the Faction’s relics are located, and Marne tells her that his research indicates they’re buried at the ruins of Civitata, the city that will soon become known as Pompeii. Meanwhile, Merytra finds that Jala has survived and saved the sarcophagus, and she and the Mal’akh thus rush to make another destination before sunrise.
The streets of Civitata are riddled with black flowers that have a curious effect on people’s memories, further evidence that the Faction’s biodata codices are leaking into the earth. Pennerton stands watch while Marne leads the others down a tunnel to an obsidian door with the Eye of Horus burnt into its surface. The rituals of the Eleven-Day Empire fail to open the door, but Marne succeeds by tracing the symbol of the Eye of Horus. Beyond is a foul stench like history rotting, and a twisted black tree with skin-like bark growing out of the shattered remains of a Faction remembrance tank. Eliza triggers a recorded message while examining the ruined equipment, and the tree itself speaks to the intruders, accusing them of trespassing on the domain of Sutekh the Destroyer.
Justine explains that the Osirian Court are powerful, god-like beings from a different timeline, whose past overlaps with the Great House’s future. Presumably, after destroying the Eleven-Day Empire, the Houses turned their attention to the Osirians, and Sutekh unleashed the Mal’akh upon Earth in response, threatening to destroy this historical focal point completely unless the Houses agreed to a truce. Justine realises that part of this truce involved the Houses handing over some of the spoils of war to the Osirians, such as the Faction’s hidden cache of biodata. Now, Sutekh’s followers have destroyed Justine’s last hope of restoring the Faction, by corrupting the hidden biodata codices, which have been used to grow the sacrificial animal with which Merytra intended to summon her god back to Earth.
The panic-stricken Pennerton arrives with a warning: the Mal’akh have come to Civitata. Justine and Eliza rush out to confront Merytra, believing that she intends to collect more sacrificial biodata from the monstrous tree -- but once the sarcophagus has been set up, Merytra orders her army to sacrifice themselves instead, and the Mal’akh spontaneously burst into flame. Their blood mingles with the corrupted biodata of the black flowers, and the sarcophagus opens into a time-space tunnel linking Earth to the Osirian Court. At last, the future that was stolen from Merytra’s people has been restored... or so she thinks until her god fails to appear. Justine tells the devastated Merytra that her god only ever used Earth as a distraction in order to force the Great Houses to make peace with his people; once that was done, the Mal’akh had served their purpose, and he lost interest in them. As Merytra collapses in tears, Eliza realises that Justine is close to losing her grip completely; not only have the Great Houses destroyed the Eleven-Day Empire, they’ve sacrificed its children and the futures that the Faction had carved out for them. Justine suspected this as soon as she saw the sacrificial animal, which is why she let Merytra escape and activate the sarcophagus -- and before Eliza can stop her, Justine leaps into the tunnel to avenge the Faction’s lost children by killing Sutekh.