The book begins with Arthur Penhaligon and Leaf attempting to return to Earth after their adventures in the Border Sea. While Leaf is able to pass through the front door and return to Earth, the presence of a Nithling duplicate of Arthur prevents him from doing so, and he is forced to remain in the Lower House.
Dame Primus then informs him that Mister Monday and Grim Tuesday have been assassinated. Moments later, he is drafted into the Glorious Army of the Architect – wherein everyone living in the House must serve for 100 years – which is based in the chessboard-like demesne called the Great Maze. The leader of the army is the Fourth Trustee of the Will, Sir Thursday, a Denizen afflicted with the deadly sin of wrath. The army is currently involved in a campaign against the Piper, who is trying to claim the Fourth Key.
Within the army, Arthur is soon mistaken for a Piper's child and has his memory wiped, along with his friend Fred Initials Numbers Gold – a real Piper's child. One month later and during the first battle against the Piper's New Nithling army, Arthur begins to recall his identity. The entirety of it is recovered later in the book when an officer mentions his name and title.
On Earth, Arthur's double, known as the Skinless Boy, has thrown a hospital near Arthur's home into panic by infecting staff and patients with a fungoid, extraterrestrial life-form which allows him to read and eventually control their thoughts and actions. This fungus, nicknamed Grayspot, is mistaken for a biological weapon, and the hospital put under quarantine. Leaf infiltrates the hospital, seeking to obtain and destroy the magical object used to create the Skinless Boy: a pocket torn from one of Arthur's shirts. She succeeds, but is infected by Grayspot in the process. She then leaves the hospital, only to find that the House has appeared above it and cannot be reached from the ground. With the help of a retired pharmacist named Sylvie, Leaf makes her way to Arthur's house where she uses a special telephone to contact Arthur's friends and get help, just as the fungus gains full control of her body.
Suzy Turquoise Blue arrives and takes the pocket to the House. There, she finds Arthur and Fred, and joins them in a raid led by Sir Thursday to find and destroy the New Nithlings' weapon; a giant spike made of nothing sitting on the center tile of the maze. The spike is preventing the mechanical floor of the Great Maze from shifting. Arthur destroys the spike by throwing the pocket into it, simultaneously destroying the Skinless Boy. As Arthur escapes from the Piper with Sir Thursday, he distracts Thursday enough for the fourth part of the Will, a snake embodying the virtue of justice, to break free, whereupon it makes Arthur the Bearer of the Fourth Key – a sword or baton depending on whether or not the wielder is in combat – and Commander of the Glorious Army of the Architect.
On Earth, Leaf wakes up in a hospital a week after the Skinless Boy was defeated. She soon learns from a nurse that the Grayspot has disappeared and that Lady Friday, another Trustee, has become a doctor on Earth.