On her 11th birthday, still grieving about her mother's death 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.
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 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 a church to try to find clues about the shoebox animals in a stained glass window.
Marnie finds a way to get the red book from the library, and when she does an old man appears and tells her that she must open to the map on page 11 and use her imagination.
When Marnie's class goes to Tantallon castle, she finds herself face to face with Michael Scot.
Marnie is reluctant to go to John Roberts' birthday party until she has a dream revealing that he is the mysterious Toledo. Then Michael Scot appears at the party as a magician and urges Marnie to undertake the quest.
Marnie leaves school in the middle of the day to try to get in touch with Michael Scot, but Toledo masquerades as the school psychologist to convince Marnie's father that she needs to be brought in for therapy.
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. Michael Scot appears to Marnie once again, trying to get her to accept the quest by talking about her mother. Then Toldeo appears, telling her that Scot is evil and is responsible for her mother's death.
Marnie hopes to find the archway on a camping trip to the Eildon Hills with her father, Dougie and Laura, but Toledo interferes.
Despite the animals' pleading with her to finish the quest, Marnie tries to catch up on her schoolwork, but then she is accused of cheating. Later, at the Pagan Mysteries, a stranger gives her the next clue in her quest.
Marnie finds a hidden door leading to the Inner Sanctum, where she confronts Michael Scot. Meanwhile, the animals decide that they must find the book on their own, without Marnie's help.
Toledo hypnotizes one of the animals to open the forbidden book. This releases evil opposites of the shoebox animals, which could destroy them.
In the season finale Marnie must make one last attempt to stop Toledo. She reveals the shoebox zoo to Laura. But when the book turns out to be a fake, Marnie's Quest continues and with a vision, she learns that it's back home. But, with two people really close to her missing, will she ever complete the Quest?
Marnie heads off back across the ocean to America, with the Shoebox Zoo and the magical Torn Page, to spend the summer with her grandparents and to continue her search for The Book.
Toledo has returned in spirit form and is and hungry to acquire a human to posses, so he can play out his evil scheme. Michael reveals the second prophecy to McTaggart and it's more deadly and terrifying than the first! There is another Chosen One, but unlike Marnie, this one is destined to become The Dawn Queen - pure evil!
Marnie goes to her grandparent's hideaway in the country with Kyle. It brings back a lot of memories for her, not least because there are so many of her mum's things still there. She also starts to have visions of a Native American girl and a European man getting married, but what could they mean?
Michael Scot's health has never been good but he is now weaker than ever and McTaggart, the true friend and servant that he is, struggles to cheer him up. Toledo also senses the old wizard's weakness and he prepares himself for the second Day of Reckoning.
Nathaniel tries to keep the strange forces from the generator at bay but he is struggling to do so. The Torn Page reveals another clue, this time it's a bear claw. The kids decide to head out on their bikes to find some meaning in this, only to be confronted by a real live bear! Luckily for them, Hunter comes to the rescue.
Marnie learns from Gramps the meaning of 'pennies in your eyes' and figures out that Michael may have died. McTaggart the weasel escapes the clutches of Taurora and makes his way to Marnie to confirm her worst nightmare - Michael is indeed dead. The Zoo are distraught - how will they ever become humans again now that Michael is gone?
Marnie and the Shoebox Zoo are perplexed by what all their clues mean. Edwin at least, is convinced that the next clue will definitely be in the form of an eagle.
Marnie heads off to camp but unfortunately for her, Gramps has also been asked to go to help out. He introduces them to the ancient Bow of Wisdom and the lost Arrow of Truth.
Marnie now realises that there could be a link between The Bow of Wisdom, the missing Arrow of Truth and The Quest. She makes it her mission to find out more. Gramps though, is more concerned about her recent behaviour. He decides he will try and cheer her up and on seeing Edwin's broken wing, secretly fixes it.
As Marnie and Kyle grow further apart, Kyle decides he must take action and he hides the Arrow of Truth. But Marnie, spurred on by Ailsa and her desperation to be human again, still manages to find it. She then goes on to steal the Bow of Wisdom from the camp, but carefully frames Kyle to take the blame.
ad confronts Marnie about her behaviour but it only serves to deepen the conflict between them and she runs off into the woods. Grandma tells him she just needs some space, but he is still concerned and heads off to look for her.
Michael visits Marnie from the spirit world, telling her that she must bring the powers of all the elements together if she is to have any chance of defeating evil.
Marnie and Kyle see the advert for Aurora's new show on TV and realise that unless they act now, all will be lost and evil will spread throughout the world. To the Shoebox Zoo's delight she brings Wolfgang back from the spirit world and he is more than happy to help out.