Mr. Magorium's (Dustin Hoffman) shoe collection runs out after 244 years and he knows that it is time for him to die. He leaves the Emporium to Mahoney (Natalie Portman) who is too unsure of herself to run it by herself and puts it up for sale.
However, when the Mutant, a.k.a. Henry their stodgy accountant (Jason Bateman), finally believes in the magic of the store, she realizes that she can provide the necessary magic for the store and reopens it.
Thanks Mary C!