“What Molly Mahoney needed was the opportunity to prove she was something more than she believed.” and so the story begins at “Mr. Magorium’s Wonder Emporium” a toy shop run by the eccentric 243 year old Mr. Edward Magorium (Dustin Hoffman).
Besides Mr. Magorium, the shop’s employees include the manager of the store, Molly Mahoney (Natalie Portman), who feels stuck in her life progress and tells Mr. Magorium that she should probably get a more adult job, and the store bookmaker Bellini (Ted Ludzik), a strongman. Eric Applebaum (Zach Mills) is a boy who comes to the toy store and regularly interacts with the adults and volunteers at the store, acting at times like a part time employee.
In response to Molly telling Mr. Magorium that she feels stuck, he gives her the Congreve Cube, a large block of wood, who tells her it will guide her to a new life and adventure if she has faith in it. She is unsure what to do with the cube at first, owing to its dull appearance. What Molly has wanted to do with her life is to become a composer and concert pianist, owing to the fact that she was a musical prodigy as a child. She went to school for music, but has not been able to write any music since graduating. At home, she works on a symphony with little progress.
The toy shop is magical. The toys have a life of their own. An over-sized ledger, known as the Big Book, can magically materialize any toy on command, and a doorknob, when rotated, can change the interior of a magic room. Mr. Magorium states that he imbued the shop with the same youthful characteristics of the children who visit it. Because of its similarity to children, the shop is also prone to temper tantrums.
Mr. Magorium suddenly announces he intends to “leave” and is giving the shop to Molly to provide her with the means to move forward and become “unstuck” in life. When Mahoney expresses her upset and doubts about her ability to run the store, the store throws a tantrum, causing all the toys and its inner workings to go haywire, ambushing customers of all ages. In preparation for his departure, Mr. Magorium hires an accountant Henry Weston (Jason Bateman), to organize the shop’s paperwork and determine the monetary value of the store he will leave as a legacy to Mahoney. Henry does not believe that the toy store is magical at all at first, arguing with Molly over its magical properties and debating the actuality of Magorium’s records.
Molly finally realizes that Mr. Magorium’s leaving is not retirement but that he is going to die. Desperate to stop this, Molly rushes him to the hospital where after a little mischief, he is discharged the next day because there is “nothing physically wrong with him.”
After leaving the hospital, Mr. Magorium asks Molly how she is doing with the Congreve Cube. She states there are a million things she could do with a block of wood but she doesn’t have a clue how to unlock the cube’s secret. Mr. Magorium then tells her that there are a million things one could do with a block of wood, but what if someone just believed in the cube? What would happen then? Molly does not understand but attempts to prevent Mr. Magorium’s departure by showing him the joys of life, but he has lived a full life and it is time for his story to end. He uses the stage notes of Shakespeare’s King Lear to make the point about a the importance of having a full life, and the importance of death, noting that the last lines of one of the most important pieces of literature are simply “He dies.”
Believing herself to be unworthy and incapable of owning a magical store, Molly puts it up for sale with Henry’s firm overseeing the sale. The store grieves and loses its magic. All the toys, walls, and even the furniture lose their color, becoming varying shades of gray and black. Eric tries to reason with Molly over her decision to sell the store when he sees her at a restaurant playing background music.
Henry meets Molly at the store to draw up the sale papers, where he sees the Congreve Cube and asks her about it. When Molly confesses her complete faith in the store and the Congreve Cube’s magical ability, the block suddenly springs to life, and proceeds to fly around the store. After witnessing this, Henry faints with shock. When he later awakes and questions Molly about it, she tells him that it must have been a dream as she went home the previous night, leaving him to finalize the paperwork for the sale.
Henry is not deterred as he knows Molly made the cube fly and though she does not believe she can do magical and wonderful things, he believes in her. Henry realizes Molly is the Congreve Cube. The block of wood that can be anything she desires if she can somehow believe in herself. Henry’s whole hearted belief in Molly ignites a tiny spark in her and for a second she believes. The store responds to her spark of belief and continues to respond as her confidence builds until the entire store magnificently transforms. The magic and color return as Molly’s symphony comes into existence. Molly Mahoney’s story has begun.