What is a word for a hidden story beneath the main one?

How about a subliminal message?

Definition 2 of Subliminal from Merriam Webster

existing or functioning below the threshold of consciousness

"Subliminal" would imply, in my opinion, that it is not outright known that the script of "Wicked" is attempting to showcase the "real story" and / or "what really happened", just a retelling from a different perspective.

Think of subliminal messaging and how only those who know what to look for will see it.

I think you might mean "subtext." See the article on Wikipedia, which contains other ideas you may wish to use instead. https://en.wikipedia.org/wiki/Subtext

You may be looking for one of

• spin-off
• derivative [story]
• adaptation

spinoff or spin-off (spĭn′ôf′, -ŏf′) n.
3. Something derived from an earlier work, such as a television show starring a character who had a popular minor role in another show.

[spinoff. (n.d.) American Heritage® Dictionary of the English Language, Fifth Edition. (2011). Retrieved December 3 2015 from http://www.thefreedictionary.com/spinoff .]

derivative (dɪˈrɪvətɪv) adj
2. based on or making use of other sources; not original or primary

[derivative. (n.d.) Collins English Dictionary – Complete and Unabridged. (1991, 1994, 1998, 2000, 2003). Retrieved December 3 2015 from http://www.thefreedictionary.com/derivative .]

ad·ap·ta·tion (ăd′ăp-tā′shən) n.
2. b. A composition that has been recast into a new form: The play is an adaptation of a short novel.

[adaptation. (n.d.) American Heritage® Dictionary of the English Language, Fifth Edition. (2011). Retrieved December 3 2015 from http://www.thefreedictionary.com/adaptation .]

Or perhaps you are referring to the allegorical meaning of The Wizard of Oz, where Wicked is understood as the underlying ("real") story conveyed by the allegory of Wizard:

allegory, n.
2. A story, picture, etc. which uses symbols to convey a hidden or ulterior meaning, typically a moral or political one; a symbolic representation; an extended or continued metaphor.

["allegory, n.". OED Online. September 2015. Oxford University Press. http://www.oed.com/view/Entry/5230?rskey=a4Lm5O&result=1&isAdvanced=false (accessed December 03, 2015).]

I think you are referring to the moral:

• the lesson or principle contained in or taught by a fable, a story, or an event.

(AHD)

Example:

• The moral of the Wizard of Oz actually comes out of anyone's personal experience. The moral is to go get your heart's desire. But be prepared for obstacles. Plus, it helps to have good reliable friends to support your quest. It is best, if you actually know what your heart's desire actually is. And be prepared for evil people to get in your way. And always watch out for those who are not what they seem. The aspects of each of Dorothy's companions and their natures is a strong key to how men were being viewed in the early 20th century. The smart/ dumb unsubstantial straw man. The kind well mannered, seemingly robotic tin man and the very gay cowardly lion. Glinda was very likely Dorothy's idea of what her mother would have been like. And the Wizard, himself, as a well meaning fraud.

Is plot (also called plotline or storyline) the word you're after?

plot: the plan, scheme, or main story of a literary or dramatic work, as a play, novel, or short story. Random House

Alternately, how about going with a phrase such as the real story behind or the bottom of the story?

Two terms come to mind as descriptions, but not as synonyms for what you're describing.

If you were to simplify your example to a single "trope", IE, a literary device, then the word you'd be looking for would be a "subversion".

Example: The trope is that the ugly woman dressed in black with the cackle is the villain. It shows up everywhere! The subversion in Wicked is that she's actually the victim/protagonist.

For "deconstruction", there are two types: The first is a work that examines all the elements of a story or genre and analyzes them academically. The second is a work that does this same examination but does so by presenting a new work that mocks/plays with/highlights the tropes and themes commonly used in the genre or original story. It can do this by subversion, as above, but also by emphasis or exaggeration of the tropes involved.

For example, Watchmen is highly regarded as a deconstruction of superhero comics, but is also a literary work in its own right.

Wicked is a deconstruction of The Wizard of Oz.

However, neither word on its own fully conveys what you want. The deconstruction doesn't necessarily mean the "flipping" that you're looking for, while "subversion" generally refers to one memetic concept or trope, not the entire work.

You could say that Wicked is a deconstruction of The Wizard of Oz that subverts many of the tropes and themes it uses, especially the trope that unattractive -> villain.

It's a secret history or shadow history.

From Wikipedia.

A secret history (or shadow history) is a revisionist interpretation of either fictional or real history which is claimed to have been deliberately suppressed, forgotten, or ignored by established scholars.

An example they give of a shadow history of a fictional world is:

"Philip José Farmer's The Other Log of Phileas Fogg reinterprets Jules Verne's famous tale with the assumption that in fact Fogg was the immortal foster child of a race of hominid aliens known as the Eridani, and that his travel around the world was part of a secret mission on their behalf."

And an example of a shadow history of the real world:

"Alexandre Dumas' last major work, The Knight of Sainte-Hermine asserts that it was the novel's protagonist who killed the British Admiral Horatio Nelson and that the true circumstances of Nelson's death were kept secret for reasons which form part of the book's plot."

I don't know whether just telling the same events from a different point of view (like The Wind Done Gone) qualifies as a shadow history, but I believe that Wicked introduces enough new revisionist background that it does.

I think you’re actually referring to an allegory

al·le·go·ry /ˈaləˌɡôrē/ Learn to pronounce noun a story, poem, or picture that can be interpreted to reveal a hidden meaning, typically a moral or political one. "Pilgrim's Progress is an allegory of the spiritual journey" synonyms: parable, analogy, metaphor, symbol, emblem; More