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Molly Mahoney (Natalie Portman) is an employee at "Mr. Magorium's Wonder Emporium", a magical toy shop run by the eccentric 243-year-old Mr. Edward Magorium (Dustin Hoffman). Besides Molly and Mr. Magorium, store bookbuilder Bellini (Ted Ludzik), a strongman, is also employed. Eric Applebaum (Zach Mills) is a boy who comes to the store daily and functions as an employee despite his young age.
In response to Mahoney telling Mr. Magorium that she feels stuck, he gives her the Congreve Cube, a big block of wood, and tells her it will guide her to a new life and adventure if she has faith in it. Mahoney wants to become a composer and concert pianist, but has not been able to write any music since graduating. At home, she works on a concerto with little progress.
Mr. Magorium suddenly announces that he intends to "leave" and is giving the shop to Mahoney to provide her with the means to move forward and become "unstuck" in life. In preparation for his departure, Mr. Magorium hires an accountant, Henry Weston (Jason Bateman), to organize the shop's paperwork and determine his legacy to Mahoney. Henry does not believe that the toy store is magical, arguing with Molly over its properties and debating the actuality of Magorium's records from the past 200 years.
When Mahoney expresses her doubts and becoming upset 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. Mahoney finally realizes that Mr. Magorium is leaving not to retire but instead he is going to die. Desperate to stop this, Mahoney rushes him to a hospital where he is discharged the next day because nothing is physically wrong with him.
After leaving the hospital, Mr. Magorium asks Mahoney how she is doing with the Congreve Cube and asks what would happen if she believed in it. Mahoney does not understand but attempts to prevent Mr. Magorium's departure by showing him the joys of life, but he knows it is time for his story to end. Utilizing the stage notes of Shakespeare's King Lear to make the point about the importance of death, Magorium states the last lines of one of the most important pieces of dramatic literature are simply "He dies." Mahoney, Eric, all the children and their parents have a funeral for him.
Believing herself to be unworthy and incapable of owning a magical store, Mahoney puts it up for sale. The store grieves and loses all its magic, becoming varying shades of gray and black. Eric tries to reason with Mahoney over her decision to sell the store when he sees her at a department store playing background music.
Henry meets Mahoney at the store to draw up the sale papers, where he sees the Congreve Cube and asks her about it. When Mahoney 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 Mahoney 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 Mahoney made the cube fly and though she does not believe she can do magical and wonderful things, he believes in her. Henry realizes Mahoney is the Congreve Cube, a block of wood that can be anything if she can somehow believe in herself. Henry's whole hearted belief in Mahoney ignites a tiny spark in her and she believes. The store responds to her belief and continues to respond as her confidence builds until the entire store magnificently transforms. The magic and color return as Mahoney's long-awaited symphony comes into existence.
Who rushes Mr. Magorium to the hospital?
Mahoney