NOTE: This great spoiler was sent in by Anonymous J.
The movie opens with a young voice explaining how Bellini of the Basement's job is to chronicle the life of Mr. Magorium. Aptly named, he lives in the basement beneath the store and writes about him day and night. The narrator explains how Mr. Magorium (Dustin Hoffman) used to make toys for Napoleon among other feats, and is extremely old.
Next, we learn about Molly Mahoney (Natalie Portman), a 23 year old woman who is struggling to find a purpose to life. In her youth she was an award-winning pianist who showed much promise, but can't seem to really pour her soul into her craft, lacking self-esteem. Her dream is to write her own piano concerto, but she works as a cashier for the Emporium, and as a quirk, often is seen playing on an imaginary piano with her fingers. On her way to work, we meet the next character to whom the narration so far belongs, a little boy named Eric who hangs out at the store often and is friends with Mahoney. Eric just recently returned home from summer camp but as Mahoney finds out, didn't make any friends (none that weren't animals, at least). She enters the store and opens up, all the toys spring to life and start whirring, spinning and moving.
She walks up a magical set of stairs into Magorium's living quarters, which are every bit as eccentric as the rest of the store, and as the man who lives inside- a mashup between Willy Wonka and the Mad Hatter of Alice in Wonderland, the endearing, eccentric, strange but loveable Mr. Magorium speaks as if his world is as normal as everyone else's. Mahoney tries to talk to him about her wanting to find another job, but he only gives her a large block of wood saying "Unlikely adventures require unlikely tools".
After another look at how the entire store seems to have every kind of toy imaginable, every kind of candy and is painted every other color, another character makes the scene. Henry Weston (Jason Bateman), every bit as dreary as his name, is the new accountant Mahoney advised Magorium to hire, to assess the worth of the entire store. Weston looks uncomfortable surrounded by sceptical children, wearing his pressed suit and parted hair. Magorium seems impressed, even though Mahoney isn't.
Upstairs, we see his office, piled all over with boxes upon boxes of papers, every receipt ever printed in the store. Weston is critical and starts questioning how he, so far, hasn't been arrested for tax ovation, but is cut short when Magorium says he's leaving. He explains that he once found a shoe in a shoestore that fit so well, he bought enough to last his lifetime... and that this, the pair he is wearing now, is his last. He then leaves, having an appointment to play marbles.
Eric, the narrator and strange little friend of Mahoney's, seems to have troubles of his own- none of the neighborhood kids seem to want to play with him, and he sits alone building magnificent things out of glowsticks. Eric notices how part of the store seems to be...disintegrating somehow.
The next day, after Eric builds a life-size replica of Abraham Lincoln out of Lincoln logs, Weston is trying to figure out the strange store and it's history. We find out that Mr. Magorium is well over 200 years old at least, having the signature of Thomas Edison. Mahoney realizes Weston is a "Just" guy, someone who thinks of things as "just" a tree,"just" a bench, or ..."just" a store, and returns home on the bus.
Magorium beings a heartfelt speech by his lonesome, directed at the store itself, like a talking-to a father gives it's son, going on about how immature the store is acting, and how, since he's leaving tomorrow, the store has to get it's act together for Mahoney, who is to inherit the store.
Eric is eating at the table with his mom, who gives him a lecture about making friends, and how he spends all his time alone at the store. Eric seems to think that everyone doesn't like him, and no one ever will. Mom tells him to just pick somebody, they might surprise him.
A sweet montage and exchange between Eric and Weston occurs, while they are separated by glass, Weston is doing his accounting work. Eric writes a note on a piece of paper, asking if Weston ever plays, and he replies on a note "not since I was a kid." Eric notes back, asking if he wants to play. Weston mouths "not right now". Eric notes "how about when you stop working?" Weston notes, "I never stop working".
Mahoney inquires about the strange black moldy looking parts appearing all over the store walls. Magorium says the store isn't taking his departure very well. Magorium explains to Mahoney that it was meant to be a surprise but the store doesn't seem to like it that way... he then reveals he is leaving, and giving the store to her. Of course, Mahoney is distraught. He keeps insisting she has the capability to run the store herself, but growing more and more distressed, keeps denying it... causing the store to grow more moldy, and toys to cease their magical movement, mobiles to grind to a halt. Suddenly, children run to Magorium and tell him their books aren't
making sense, how the fingerpaints have lost their colors, paper planes drop to the ground, balls to lose their bounce. Disaster has struck, things are blowing up, and a monkey is attacking children. Pure mayhem. Eric tries fruitlessly to calm everyone, but Magorium solves the problem by shutting the store down, calling a meeting between Mahoney, Weston and Eric, and telling Weston the commotion was the store having a Temper Tantrum (being in habited by children makes the store prone to acting like a child). Weston lets slip to Mahoney that she is in his will, and it dawns on her: he is going to die.
Mahoney then makes the ultimate betrayal, taking Magorium to a hospital. Of course they don't question her saying he is delusional, saying he works in a magic toystore, that he is over 200 years old, etc. Even Weston sees error in this decision. Eric tries to talk to Mahoney, but understands that either Magorium goes to the old folks' home, or his life could be at risk. Magorium tells Mahoney before she and Eric leave, that the block of wood he gave her will give her the answers she needs, if she only believes in it. The doctor tells Mahoney he is fit physically and so must be discharged in the morning. The scene ends with the doctor turning Magorium's hospital room light off... and the entire room is covered in glow-in-the-dark stars.
The next day, Weston apologetically offers to run the store for the day, and when Mahoney asks him if he "sees anything sparkle" in her, he awkwardly tells her that her eyes do. She says that wasn't what she meant, and leaves Weston to smack his forehead with his briefcase.
Mahoney has a day of adventure with Magorium, playing with coo-coo clocks, bouncing on beds in a mattress shop, dancing on a matt of bubble wrap, among other fun things, until Magorium catches on. Mahoney excuses herself, saying it was just to show him all the things he'll be missing if he leaves, but he insists he knows that it was to make his last day perfect. The last thing he needs to do is to make a call from a public phone, which he does, to Eric, telling him that his hats are awesome, and that he needs to make friends.
Eric and Weston close up for the night, and Eric takes Weston to his
place to show him his hat collection after he remarks about Eric's
constantly changing hats. Eric opens his bedroom door reveals dozens
of hats, strung up everywhere. His mom comes home and Weston leaves,
but not before Eric calls him his friend.
Mahoney and Magorium return to his shop, which is mostly dark, being shut down for the day. Mahoney is suddenly overcome with emotion and begs him not to leave. Magorium delivers another one of his heartfelt speeches, comparing his life to a book: at the end, you don't feel sad because the book ends. You feel sad because of all you have read BEFORE the ending. What Mahoney needs to do, is keep reading. Mahoney leaves wordlessly. Magorium, finally alone with his store, strolls around one last time, looking at his legacy of toys, lit up by glowing stars. He sits on a colorful bench and says tearfully as a paper air plane lands at his feet:
"...Goodbye, my love".
Every child who ever visited his store, young or old, shows up at his funeral. Afterwards Mahoney and Eric return to the store, to see everything completely colorless. Mahoney goes to leave, but Eric, showing since far unknown emotion, begs her to stay. She leaves anyway. On the bus home she no longer plays her imaginary piano. Bellini shelves the last tome of Magorium's biography.
A supposed short time later, Eric finds Mahoney playing the piano in a hotel as a gig to make money. He wonders why she can't just run the store to make money, but Mahoney says she is selling it, and still insists she hasn't the magic to run it. Eric tells her mysteriously- that's the whole reason why Magorium gave it to her. Eric tries to buy the store himself with his allowance from Weston while Mahoney keeps showing potential buyers the property. Weston comes to inform her about Eric's offer, and finally gets Mahoney to admit she believes in the store and that everything within it is magical- and suddenly, the block of wood Magorium gave to her to begin with, springs to life! The cube soars around the shop, zooming around the stairs and the toys, until it stops in front of Weston... making him pass out inexplicably.
Mahoney wakes him up, but insists everything was a dream, and that she is still selling the store, she had left him there to handle paperwork the night before. But Weston has seen the light, and tells her it's not the store, or the cube, or anything that she needs to believe in... it's herself.
Suddenly, Mahoney hears a tune. She plays along with it on her imaginary piano, and as she moves her fingers, all the magic and color comes back to the store, exploding in sparkles and feathers. The toys spring to life as before, and as she dances around, glitter and bubbles rise from everywhere, toys dance around her feet. It's finally come to Mahoney, the concerto she wanted to write is right here, in the store, and most importantly, in herself, all along.
The movie ends with Eric's narration returning as light and color surround Mahoney-
"And that... is how Molly Mahoney's story began."
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!