December 1951: Workmen renovating a Blitz-damaged building near Spitalfields Market, where Emily Blandish first appeared out of the fog, find the skeletal remains of a woman who appears to have had occult runs carved into her body. Honoré reads of the discovery, and feels drawn to investigate even though he and Emily haven't spoken for weeks since their encounter with their alternative selves. Emily, who had been planning to visit Honoré and try to make peace with him, sees him leaving his home and follows him to the morgue. There, Honoré is sent reeling by his sight of the body; the woman was wearing clothing made of material that won't be invented for over 50 years, the runes were carved into her flesh while she was still alive, and the body has a time-snake unlike anything Honoré has ever seen before. He and Emily quickly settle their differences, both aware that what's happening here is bigger than their disagreements, and they leap along the body's time-snake moments before Inspector John Harris and Dr Morrow enter the morgue to examine the body themselves.
Honoré and Emily find themselves in a ruined city stalked by creatures like stone gargoyles brought to life -- and when they see the ruins of Big Ben, they realise that this is London in the distant future. Despite their experiences with their alternative selves, they agree that something about this future seems wrong, as if it should never have come to pass, and both agree to try to prevent it from happening. They are then attacked by one of the gargoyles, which vapourises their cover with a blast of heat from its hand, but the gargoyle is then blown to pieces by three human soldiers. The soldiers get Honoré and Emily to safety in the sewers before the gargoyle can reform itself, but when they realise that Honoré and Emily are newcomers, they reveal that time-travellers seem to be drawn to this era and that the gargoyle deliberately targeted them. The soldiers allow them to shelter briefly at a shantytown in the ruined Houses of Parliament, but warn them that they must leave before they draw the gargoyles here. Before they go, they learn that this future was apparently brought about when a secret society called the Sodality made a deal with the Devil and then tried to renege on it.
Elsewhere in the ruined city, the High Executioner of the Sodality meets a stranger named Dr Smith. The Sodality once bred human time-sensitives and time-channellers, but the creature that they worship, Mastho, then declared their experiments an abomination and threatened to destroy the world if any remained when he returned. The Sodality have attempted to purge the results of their experiments from history, but a few channellers and sensitives remain -- including the High Executioner herself. Dr Smith claimed to have come to help exterminate the surviving channellers and sensitives in order to save the world, but once alone with the High Executioner, he looks her in the eye and tells her that she's not a bad person; she was betrayed by a duplicitious lover and brainwashed by the Sodality, but given the chance to live her life over again, he knows that she'd help others rather than harm them. She is tempted to let Dr Smith help her, but the Grand Master of the Sodality has been listening and intervenes before she can decide. He has Dr Smith confined to the "guest" quarters, but despite his concerns, he doesn't dare speak against the High Executioner for fear that she will have him executed. However, he warns her to deal with any outstanding issues before they summon Mastho again... in three days' time.
Back out on the streets, Emily and Honoré follow a lead to St Paul's Cathedral, which is rumoured to be haunted. Flayed human torsos have been strung up outside as a deterrent, but the Cathedral turns out to be deserted apart from a small campsite. A woman named Maria suddenly materialises in the camp, and when Honoré and Emily see the runes carved into her flesh, they realise that she's the woman whose body they have already found in 1951. Maria is initially wary of them, but decides to trust them and tells them about the origins of the Sodality. The Cabal of the Horned Beast, the secret society that Emily and Honoré encountered in Victorian London, was originally founded as an excuse for gentlemanly debauchery, but some of its members started to take its rituals seriously. They found a book of ancient magic that enabled them to control Time and summon demons; the book was stolen in the 20th century, but the surviving members of the Cabal eventually got it back and learned its secrets. Using the psionic sciences in the book, they began to travel through Time, conducting experiments to breed time-sensitives and time-channellers, and changing their own past to turn the insignificant Cabal into the all-powerful Sodality. But their meddling caused history to collapse in on itself, creating this devastated future, and now the Sodality have turned against their creations, hunting down and killing all of the sensitives and channellers that they'd created. Maria herself is a product of their experiments; she was kidnapped from 16th-century Venice and tortured, and the runes carved into her flesh have given her the ability to leap back and forth from Venice to this devastated future. However, she is unable to travel anywhere else, and is unable to control when she leaps.
Unsure how to tell Maria that they've already seen her dead body, Honoré and Emily simply tell her that they need help to stop the Sodality. Maria agrees to carry them along the next time she jumps back to 1586, which occurs a few hours later. Back home in Venice, Maria has established a safe house, where her contacts -- a thief named Roberto and a tailor named Marco -- inform her that the Sodality will soon be holding an important masked ball. Marco has also heard that the Sodality has been conducting experiments on children beneath the Palazzo Bembo. That night, Honoré and Emily see a living gargoyle attack a woman in the street; Honoré tricks the gargoyle into falling into the canal, and the terrified woman reveals that she was targeted for speaking out against the Sodality's plan to summon the Devil while their experiments have not yet produced the Child of Time. The woman flees, realising that she's said too much, but the phrase "Child of Time" resonates with Emily. Already suspecting that the children beneath the Palazzo Bembo are related to the Peculiar, Emily now wonders if she's one of them; perhaps she herself is the Child of Time. She thus decides to rescue the children while Honoré and Maria attend the masked ball.
Emily breaks into the Palazzo Bembo through a servants' entrance, but is caught by a guard and thrown into a cell. However, when the Grand Master of the Sodality sees her, he frees her instantly, apologising profusely for the guard's mistake. Realising that she's benefited from a case of mistaken identity, Emily plays along, but slips away once she gets the chance. She then hears the voice of her Peculiar friend Violet in her head, guiding her to a secret chamber beneath the palace, where children are being tortured by surgeons in the employ of the Sodality; some have runes carved into their flesh, and some are being turned into mechanical hybrids like Abraxas. The Grand Master is ordering the chief surgeon to prepare his best test subjects for tonight's summoning; if they find favour with the Devil, the Sodality will share in his power. Once the Grand Master has gone, Emily finds her Peculiar friends Violet, Jimmie, and Freia, locked in cells bound up by psionic science; most of the other Peculiars were killed by the Sodality, and although Percival escaped, he is now lost in time. Emily decides to play on the case of mistaken identity again, and emerges from hiding and orders the surgeon to release the children; he does as ordered, and once the psionic bonds are free, Violet knocks him out with a thought. Emily stops her from taking revenge by killing her way out of the Palazzo, telling her that she must control her rage instead of punishing innocents. Violet accepts this, and once free of the Palazzo, the three children vanish through Time while Emily returns to the safe house to wait for Honoré and Maria.
Marco has made 100 masks for the ball, and when the Comte di Meglio arrives at his shop to collect them, Honoré and Roberto ambush him and force him to reveal all he knows about the ball. Unsurprisingly, it's to be held at the Palazzo Bembo; the Sodality intend to summon the Devil at midnight, in the hope that he will grant them his powers in exchange for the Child of Time. Honoré takes two masks so he and Maria can crash the party, and on the way, she reveals that, perhaps thanks to Honoré's calming influence, she's been learning to control her own time jumps. Neither of them believe that the Sodality will really summon the Devil, but when the Grand Master and his Chancellor arrive, that's exactly what happens. One of the living gargoyles kills a man who'd been suspected of speaking out against them, just as an example to the others, and the Grand Master and Chancellor then conduct a ritual with chanting and blood sacrifice... and a Daemon named Mastho materialises in the great hall.
The Grand Master presents the time-sensitive children, expecting to be praised, but Mastho unexpectedly declares them abominations; his people have been conducting their own experiment with humanity, and the Sodality's meddling has corrupted it. Mastho incinerates the children with a wave of his hand, but offers the Sodality a chance to correct their mistake. Due to the non-linear nature of Time, this is the second time he's been summoned although the Sodality believe it to be the first; he will appear once more, in exactly 1000 years, and if the Sodality has not destroyed all surviving time-chanellers and sensitives then he will declare the experiment a failure and destroy the world. Mastho vanishes, and the Grand Master, shaken, nevertheless spins this event to his benefit. He assures his followers that they will still share in the Daemon's power once their task is complete, and they will continue their experiments to create the Child of Time in the hope that this will help them to hunt down and destroy all the remaining time-sensitives and channellers. From now on, the Chancellor -- who is herself a time-channeller -- will be known as the High Executioner. The followers scatter as the ball comes to an end, and Honoré and Maria return to the safe house and share stories with Emily. Maria then feels herself beginning to phase again, and transports Honoré and Emily back with her to the ruined London of 2586.
In the ruined city, the Sodality is preparing for the third and final summoning; they have already attempted an experimental second summoning, which, due to the non-linear nature of time travel, was Mastho's first. The High Executioner has travelled through Time with the Grand Master, hunting and killing the results of their experiments, and she's come to revel in the carnage... but some part of her, buried deep down, is horrified by the monster that she's become. This is the part that Dr Smith has been trying to reach; he never really intended to help kill the Sodality's innocent victims, and only used that as a pretext to speak to the High Executioner in person. Haunted by what he's said to her, the High Executioner visits him once again, and he offers her a choice: help him to set history right so that the Sodality never exists, and he will give her the opportunity to make a better life for herself. She demands proof that he can do what he claims, and he steps into the other room of his suite. Moments later, she hears an odd wheezing groaning noise, and enters the room to find that Dr Smith has vanished into thin air.
Honoré, Emily, and Maria materialise back in St Paul's Cathedral to find that the Sodality have chosen it for the location of the third summoning. Fortunately, they are not spotted arriving, but the human soldiers who helped Honoré and Emily when they first arrived investigate the activity at the Cathedral and are killed by the gargoyles. The Grand Master and High Executioner arrive, masked as before, but Honoré catches glimpses of their confused time-snakes and realises that the High Executioner is directly responsible for the slaughter of countless innocents in the Sodality's purges. The summoning takes place, and when Mastho arrives, he reveals that he already knows that the Sodality's purge has failed -- because he captured Violet, Jimmie, and Freia as they attempted to escape from Venice. As Mastho speaks, Honoré sees that the time-snakes of everyone in the Cathedral have suddenly become truncated; no one here has a future any more.
The High Executioner promises that the Sodality will still fulfil their promise, and Mastho orders her to prove her loyalty by killing the Grand Master with his own sacrificial dagger. She does so without hesitation, but Mastho just laughs at her and reveals that he's played the Sodality for fools. The purpose of the Daemons' experiment with humanity was to create a human with the powers of a time-sensitive and time-channeller combined; they intend to study her, take her powers for themselves, and thus become the new masters of Time. Mastho never considered the Sodality's experiments a failure; he simply ordered the purges in order to create an environment where only the most accomplished of the channellers and sensitives would survive. The Child of Time has been forced to achieve her full potential in order to hide from them, and the Daemon now summons her to his side. Before Honoré's and Emily's eyes, Maria is transported down from the balcony and transformed into a glowing, angelic being -- the Child of Time. In this moment of the Sodality's utter failure, the High Executioner sees Dr Smith step out of the shadows, and in her rage she rips off her mask to confront him... and the horrified Emily recognises herself.
Mastho dismisses the Sodality from his concern and prepares to take the Child of Time back to his home world -- but before he can bind his powers to Maria, she reveals that she still has free will, and vanishes. The enraged Mastho lashes about in frustration, catching the High Executioner a glancing blow and knocking her senseless. Dr Smith, deliberately glancing up at Honoré in the balcony, picks up the unconscious Executioner and carries her back to his Cabinet of Light, taking her away from St Paul's Cathedral. Maria, now fully in control of her powers, nevertheless believes that there's only one escape from Mastho -- the escape she longed for throughout years of torture at the Sodality's hands. She thus follows the Cabinet of Light back to London in the year 1949, materialises in the damaged building in Spitalfields Market, and uses her powers to bring the ruined building down completely and crush her to death.
Emily, horrified to learn what kind of person she really is, throws herself from the balcony before Honoré can stop her -- but in the confusion, the Peculiar children have escaped, and Violet psychically cushions Emily's fall and soothes her troubled mind. Emily will still remember what she used to be, but the memories will not torture her, and she can continue to be the good person whom Honoré has known. Mastho then senses Maria's death, and begins to convulse; he can no longer bind his powers to Maria as he had intended, and the laws of psionic science are causing those powers to turn back on him. Honoré and Emily time-jump away from St Paul's as Mastho's body explodes with power, razing the Cathedral to the ground. Before returning to 1951, however, they stop off two years prior to watch as "the girl in pink pyjamas" -- the former High Executioner, Emily Blandish -- stumbles out of the fog in Spitalfields Market, suffering from amnesia. This is where their adventures began, and Honoré and Emily return to 1951, where new adventures await.