On her 11th birthday, still grieving over her recently deceased mother and uncomfortable with being moved from Colorado to Scotland, Marnie discovers that she is able to make a group of four old toy animals come alive.

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.

Since Marnie's suggestion to go to Tantallon Castle was agreed on by majority vote, her class goes there for a field trip. While exploring the castle, Marnie goes off the beaten path and finds herself face to face with the great wizard Michael Scot.

Marnie is reluctant to go to John Roberts' birthday party until she has a dream revealing that he was really the evil shapeshifter Toledo all along, and so she plans to confront him. However, things take a strange turn when Michael Scot appears at the party as a stage magician.

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.

Marnie and Wolfgang confront Michael regarding the events that lead to the creation of the Shoebox Zoo. Meanwhile, the other animals decide that they must find the book on their own, without Marnie's help, and so they head to the University Library in an attempt to solve the next clue.

Toledo hypnotizes Edwin and orders him to open the Book of Forbidden Knowledge. The dark energy released from inside the book awakens the shapeshifter’s devious creations, which are shadowy dopplegangers of the Shoebox Zoo made to destroy them.