An unexploded bomb from the Blitz is detonated during a botched defusing attempt, revealing an underground cavern just beyond Constitution Hill station. The monstrous creatures that live in the cavern begin to emerge at night, seeking sweet food and killing and eating anyone who gets in their way. Soon afterwards, Honoré and Emily are contacted by Randolph Crest, a small, toad-like poet who claims that the Subterraneans, subhuman creatures from his poetry, are stalking him. Both Honoré and Emily can sense something strange about Randolph, but their client has an aversion to being touched, and refuses to discuss his private life with them, even though he somehow expects them to save his life.
Honoré investigates the Subterraneans’ activities, and discovers that they have begun to commit deliberate murders. One man is drowned in a park fountain; another is thrown from his window and killed from his fall through the air. Emily determines that the murders are connected by the victims’ names and birth signs, and concludes that the next two victims will be a Taurus killed by earth and a Leo killed by fire. Determined to learn more about Crest’s connection to the creatures, they attend a poetry reading that he has reluctantly agreed to give in public. During the performance, Crest suddenly suffers a strange fit and recites a weird poem unlike any of his other work. He is taken to the hospital to recover, but Emily realises that the names of the Subterraneans’ past and future victims are encoded within the poem.
Emily and Honoré are too late to save the third victim, but they do manage to capture one of the Subterraneans as it flees the scene of the crime. Honoré takes it back to his apartment, where he pacifies it by feeding it chocolate. When he tries to read the creature using his time-sensitivity, he is confused by the impressions he receives, but Emily interprets them to mean that the Subterraneans possess a collective intelligence like a swarm of bees; the swarm possessses an intelligence that the individual members do not. Honoré manages to read the collective’s future, which leads him and Emily to their next and last victim, a man named Cionadh.
Cionadh refuses to listen to them and kicks them out of his house, and when they try to press their case, the neighbours call the police. Honoré and Emily are locked up, questioned, and released -- but in their absence, Cionadh has been kidnapped by the Subterraneans. Hoping to rescue him, Honoré and Emily use the creature they captured as a guide, and it leads them into the sewers -- where they find that Cionadh has been tied to a pyre before a giant, demonic statue surrounded by Subterraneans. The Subterraneans are being directed by Mestizer, who recognises Emily at once and reveals that she’s been stranded in London since their last encounter, looking for a time-channeler to help her escape. Unaware that Emily was still at large, Mestizer made contact with the Subterranean gestalt, which also has the power to perceive time in a non-linear fashion. She also learned that the Subterraneans were searching for their missing leader, the core of their gestalt mind, who had escaped into the outside world. She thus offered to give the gestalt a new corporeal body in exchange for its power.
Before Honoré can stop her, Mestizer sets Cionadh alight, killing him with fire, completing the ritual and allowing the Subterranean collective intelligence to possess the demon statue. Honoré tosses a chocolate bar towards it, and when it misses the throw and smashes through the floor to get at it, the entire cavern collapses. Mestizer is killed, but Honoré and Emily escape and make their way to the hospital, realising that Crest is the Subterraneans’ missing leader. The demon emerges from the cavern and smashes its way through London to reach Crest, but before Crest can flee, Honoré touches him, perceiving enough of his past for Emily to take him back to the moment when Crest found his way out of the caverns, dimly perceiving that there was a better life in the world above. Emily knocks out Crest as he tries to flee his fellows, and she and Honoré block the escape route, thus preventing Crest from getting out of the caverns in the first place. When Honoré and Emily leave, they forget their torch behind, and when Crest awakens he uses it. The sight of his fellow Subterraneans is such a shock that he concludes it was better for him to live in the darkness, unaware of the horrors shown by the light.
Emily and Honoré return to 1949, and although the bomb does explode and expose the cavern again, this time the Subterraneans have no reason to emerge. Mestizer thus never makes contact with them, and thus does not die in the collapsing sewers. However, Honoré and Emily can still remember the events they lived through, even though they never happened now, and they fear that the time-sensitive Mestizer, who is presumably still alive out in London, may remember these events as well and come looking for them.