It's Marnie's first day of school at her new home in Scotland. She has an encounter with a bully but makes a new friend in Laura. Back home, she receives a package from America containing a necklace that belonged to her mother. She also discovers that her shoebox animal friends were once human, and that only a lost book can return them to their original form.

When a mysterious problem causes school to be cancelled for the day, Marnie and Laura visit the nearby St. Giles’ Cathedral in order to find clues about the shoebox animals, as John Roberts said he saw a depiction of them on a stained glass window there.

Marnie manages to get the red book she was looking for from the library, after which a familiar old man appears before her and says that she must make use of a peculiar looking map that’s within the contents of the book.

Marnie leaves school in the middle of the day to try to get in touch with Michael Scot, while Toledo tries to convince Marnie's father that she needs to be brought in for therapy, as he plans to manipulate her into giving him the Book of Forbidden Knowledge while masquerading as the school psychologist.

Marnie is on a class trip to visit a "stately home," and uses her new powers to defeat a bully, but the shoebox animals become separated from her and find themselves trapped in the basement.

Marnie hopes to find the archway shown on the clue she just received, and plans to do so while on a camping trip to the Eildon Hills with the help of Dougie and Laura, but things go awry when Toledo interferes.

The shoebox animals plead with Marnie to continue the quest, but she insists on trying to catch up on her schoolwork after largely neglecting it. Despite her efforts, she gets falsely accused of cheating during a test, leading to further drama with the school principal.