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.

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 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.

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 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.

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?