The morning after Richard rescues the girl, Door, from the streets, she is greatly recovered, and sends him on a quest to find the Marquis de Carabas, a man who will be able to help Door evade the attention of the infamous and seemingly inhuman assassins, the Messrs. Croup and Vandemar. Richard is successful, and brings the Marquis back to his apartment to meet Door, only to see both curious individuals vanish immediately. The next day, Richard begins to realize the consequences of his actions. He appears to have become an invisible non-entity; he loses his job, where no one seems to recognize him, and his apartment is rented out to other people even as he bathes in its bathtub. Perhaps the strangest part of this, however, is that nobody readily acknowledges his presence, and even those dearest to him, such as his fiancée and his best friend, are unable to recall who he is. Determined to set things right, and become a part of his world once more, Richard sets out for the world of London Below in search of Door.

Richard’s journey takes him through the realm of the Rat-Speakers, who worship and perform tasks for rats, across the mysterious Night's Bridge, whose darkness takes a toll in human life from any party who crosses, and eventually to the Floating Market, where he meets again with Door, who is holding an audition for bodyguards. At this point, the legendary bodyguard and fighter Hunter joins their party, and the group, consisting of Door, the Marquis and Hunter, with Richard confusedly tagging along, sets out for the Earl's Court. While Richard has been attempting to reconstruct his life in London Above, Door and the Marquis have travelled to Door's home, and discovered a diary entry made by Door's father, which advises her to seek the angel Islington. When the four reach the Earl's Court, on a mysterious underground train which follows its own bizarre schedule, the Marquis is forced to leave due to an old grudge between himself and the Earl, and the rest discover that they need to travel through the Angelus, a mysterious artifact, in order to reach Islington (the aforementioned angel), and that the Angelus resides in the British Museum.

Door and Richard travel to the Museum, while Hunter, due to a curse which prevents her from entering London Above, remains in the abandoned British Museum underground station. After some searching, and a nearly disastrous encounter between Richard and his former fiancée, they find the Angelus, which Door "opens" using her family's special power, and travel through it to the underground home of the angel. Islington speaks to them at length, explaining that his position as protector of London Below is a punishment for the submersion of Atlantis, which was also under his care, and telling Door that he will help her learn the identity of those who killed her family—for a price. She and her company must retrieve a unique key from the Black Friars, before they return. The two return to the Museum, reunite with Hunter, and make their way to the Floating Market, where they are due to meet the Marquis.

In the meantime, the Marquis has sought out Croup and Vandemar, and has made a deal with them—in exchange for a priceless Tang dynasty figurine (which Croup, evidently a collector, promptly devours), the Marquis is given information regarding who ordered the murder of Door's family. The true price for this information, however, is his life—Croup and Vandemar catch, torture, and kill him, breaking the one-hour "head start" agreement that was part of their deal with the Marquis. Door, Richard, and Hunter proceed onward to the dwelling of the Black Friars. There, they are forced to defeat a series of three ordeals; Hunter wins a test of strength, Door wins a test of intellect, and Richard, alone in history, wins a test of constitution of character, and as a result, the three succeed in gaining the key. They then travel to the floating market, where they are unable to find the Marquis, but where Hammersmith, a blacksmith friend of Door's is able to forge a copy of the key won by Richard. They enlist the mysterious Lamia, one of the vampire-like Velvets, as a guide, and set foot on their final path, toward Islington.

As Door, Richard, Lamia, and Hunter make their way down the long path of   Down Street, a friend of the Marquis' named Old Bailey finds and revives his corpse, using a stored portion of the Marquis' life, and the Marquis sets out himself, following Door and company. On Down Street, we discover that Lamia was a dangerous choice for a guide, because the price she demands of Richard for his services is higher than he can pay and yet live, but she is driven away by the weakened, crossbow-wielding Marquis. We also discover that Hunter long ago turned traitor to Door’s cause, when she gives Door to Croup and Vandemar, in exchange for the magical spear she needs to follow her calling and namesake, and hunt and slay the great Beast of London. Croup and Vandemar, with Door captive, travel onward and downward, while Richard, the Marquis, and Hunter travel at a slower pace, all toward the great mud- and sewage-filled labyrinth through which they need to pass to reach Islington. It is in this labyrinth that the Beast dwells, and Hunter and Richard manage to kill it and pass through the maze, although the Beast's death is at the price of Hunter’s own.

Richard rushes ahead, to the final confrontation between the parties, in which we learn of Islington’s true nature. Islington wishes to use Door and the key to force open the door to Heaven, where he seeks dominion over all the other angels as revenge for his banishment. After Richard is tortured by Croup and Vandemar, Door agrees to open the door, but unbeknownst to her captors, she uses the copy of the key Richard won to open it, and it does not open it to Heaven, but instead to somewhere else, as far away as she could, possibly Hell. Islington, Croup and Vandemar all disappear through the gateway before Door closes it. Door then uses the Black Friars' intact and magical key to allow Richard to travel back to London Above, and a London Above in which he is known and recognized. After returning home, Richard is happy for a time, but he realizes that his experiences have changed him, and that his old life and friends mean little or nothing to him now. The story ends with his joyful return to London Below, where he takes up the title "Warrior of London Below" in recognition of his having slain the Beast of London.