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.

Marnie makes one last attempt to stop Toledo from taking the book, and comes out victorious after realizing that the book was a fake created to seal the evil shapeshifter’s magic all along. She then learns that the location of the real book is somewhere back home in Denver, and that she must return there in order to continue the Quest.

Marnie, with the Shoebox Zoo in tow, flies to Denver for the summer in order to search for The Book of Forbidden Knowledge. After being picked up by her grandparents, she meets up with her best friend Kyle Stone and plans to show the shoebox animals to him. However, a mysterious figure has stolen the bag in which they were contained, on top of seemingly following her around wherever she goes.

Kyle finds Marnie’s bag on his way to visit her for breakfast. With the proper bag now on hand, Marnie introduces Kyle to the shoebox animals and tells him about the Quest. Later, they’re taken a TV studio where they meet Aurora Dexter, a medium who aspires to become a TV star.

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.

Marnie and Kyle go to watch a rodeo. While there, Kyle confides in Marnie regarding his self-doubts as well as his reluctance to keep going with the quest, which leads to an argument between the two.

Marnie goes to Camp Healing Bow along with Kyle and some of her former classmates. Following their arrival, they partake in several fun activities, but Marnie suddenly starts exhibiting hostility towards everyone around her and no one seems to know why.

The stay at Camp Healing Bow continues. Marnie’s odd behavior seems to worsen, which puts a strain on her friendship with Kyle. Despite this, the two agree to investigate the next clue, an eagle rune, together. Meanwhile, Marnie’s father arrives in Denver to visit her, but things take an unexpected turn when Aurora picks him up at the airport.

It’s the last day of camp, and Marnie’s father comes to visit her. However, happiness quickly turns to anger when Marnie sees that he’s brought Aurora along with him, and that they’ve seemingly fallen in love with one another.

The Quest’s conclusion draws near, with only one clue remaining unsolved, the wolf rune. Marnie, now fully consumed by her anguish and grief as a result of the book’s corruption, is desperate to take the book so she could revive her deceased mother, and uses any means necessary in order to reach it.

All hope seems lost as the book has fallen into Toledo’s hands. However, upon receiving some encouraging words from a fallen ally, Marnie comes to the realization that the book must be destroyed in order to save the world, and so she ties up some loose ends in preparation for the impending final battle.

Marnie, Kyle and the Shoebox Zoo all band together in order to put an end to the Dawn Queen’s evil plans once and for all. Can they truly destroy the book before it plunges the world into chaos? And what will become of the shoebox animals if they succeed?