[1] The book continues the story of the young house mouse Audrey after she and her friends have defeated the evil cat Jupiter, lord of the sewer rats.

Albino mouse Oswald Chitter is deathly ill, having caught an infection during his time in the Deptford sewers battling the villainous cat Jupiter with his friends.

Midshipmouse Thomas Triton arrives with news that the Starwife, the wise and ancient queen of the squirrels, has summoned Audrey to her chambers so she can hear the story of Jupiter's downfall firsthand.

While there, the Starwife reveals the main reason for summoning Audrey: the rat Madame Akkikuyu was found wandering aimlessly in Greenwich Park by her sentries.

Now she is harmless, and the Starwife believes it best if Audrey, whom Akkikuyu considers her close friend, accompanies the rat to Twit's home of Fennywolde, a rural field.

Upon her arrival in Fennywolde, Akkikuyu immediately gains the respect of the inhabitants by saving the lives of two fieldmouse children and chasing off the owl who attacked them.

Jarvis has said he based Fennywolde on the fields of a farm he played in as a child: "Everything in the book was there, the meadow, the ditch and the pool surrounded by trees.

"[3] Sally Estes of Booklist said that The Crystal Prison "lacks the power of its predecessor, but it still stands up well as a foreboding bridge to the trilogy's concluding volume.

"[4] According to Eva Mitnick of School Library Journal, "Although this book stands on its own, readers who aren't familiar with the first volume might become impatient with the first section, which introduces a multitude of characters and moves slowly, impeded by old-fashioned, florid prose.

The pace picks up in the countryside, where an ever-hungry owl and the mysterious spirit bring menace and tragedy to the close-knit community of field mice who live there, and the final chapters are breathtakingly thrilling.