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 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.

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 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.

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?