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.

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 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.

After settling in a hideaway that’s owned by the Campbells, Marnie and Kyle go to investigate the first clue, a snake rune, at the nearby Snake Creek Trail. After an argument causes the two to split up, Marnie has an encounter with the ghost of Toledo, the shapeshifter.

Marnie and Kyle go to a Native American festival called “The Pow Wow”. While there, Marnie comes face to face with the mysterious figure who’s been following her around since she arrived back in Denver.

Marnie and Kyle go bike riding in the woods in order to investigate the next clue, a bear claw rune, but things go awry when the shoebox animals fall out of Marnie’s backpack and are spotted by a wild bear. Meanwhile, Toledo puts his plan to bring about the second prophecy into motion.

It’s Kyle’s 12th birthday, and so Marnie attends his birthday party. Toledo, now possessing Aurora’s body, spies on Marnie at the party and encourages her to find the book, attempting to allure her with the prospect of unlimited power.