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, 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?