-Writers Notes-
Well, I'm not much of a writer, nor a deep MLP fan, but I do like to construct animations.
MLP:FIM seems to have a well structured narrative, fluent and fun for all to enjoy, and this fiction is to act as a special feature-length episode.
Though it isn't cannon to the actual MLP:FIM story, it's an OVA (Original Video Animation) of what could of happened in the narrative- perhaps as a season finale.
This idea is pretty old now, and I always said "I'll write it later"...and here we are 5 Months Later.
If I could, I'd give them this story to see animated. Since I can't, I give it to you to imagine the scenes yourself.

*Also! I hope the spelling isn't too bad as I'm using MS Notepad to start them and upload them from it.

-What the Story Contains-
Can't be bothered to read it all?
Here's an actual list of what actually happens in this feature-length episode; showing a hidden connection between Twilight and Luna, whilst revealing the past between the Two Princesses and the God of Discord.
I must warn you though, this list is pretty much a spoiler.

[#1] Twilight and Spike holds a gathering with their friends at the newly opened magic Gallery of Ages in upper Canterlot as a way to surprise them each with a unique unknown gift.
[#2] Unaware to the events to happen on this day, Twilight triggers an unknown Statue's magic trap which teleports her to a Past Equestria, unable to give her friends the gifts.
[#3] A younger Princess Luna and Twilight meet, only to cause confusion to the scenario Twilight finds herself in.
[#4] Twilight tries to get a meeting with the young Celestia, only to realize she isn't all that generous as she seemed to be.
[#5] Twilight learns from Celestia's harsh words and from the kind words of Quin and Elgon what happened to the previous King.
[#6] Luna, still wandering the wilderness goes off and finds herself somewhere in the Everfree Forest- only to be re-confronted by The Shadow People.
[#7] After years of whispering to her, The Shadow People finally persuade Luna to overthrow her sister to give her the respect that she deserves.
[#8] Luna is persuaded to goes with Twilight to speak with Celestia, only to have Luna tricked in allowing The Shadow People to pass through the Castle's Barrier and take control.
[#9] The Shadows thank Luna, collectively taking a physical form similar to a Pony: this is the creation of the Draconequus.
[#10] Twilight confronts the beast, calling it "Discord". The Draconequus dons the name and starts to cause chaos.
[#11] Celestia is turned to stone by Discord's magic and assisted by the heartbreak of Luna's actions, while Twilight alone is shown to be helpless.
[#12] The confused Luna is upset by her actions and Discord throws the 'Crybaby' and Twilight out of the Castle, only to have it become uprooted like a tree and ascend to the sky.
[#13] Ignoring Twilight's comfort, Luna goes of to find a way on her own: trusting no one. The lone Twilight goes seek help.
[#14] After meeting in a safe location with Quin and Eldon, Twilight believes she can form a resistance to fight against Discord's personal horde of Timberwolves which have started to spread darkness throughout Equestria.
[#15] With no idea on where to start, Luna appears bringing 6 Round Gems from the Canterlot Cathedral. This gives the well informed Twilight an idea.
[#16] The resistance is officially formed with Twilight's confidence: Quin and Eldon, the retired Commander Hurricane and her army, the hesitant Luna and Twilight herself.
[#17] The corrupted Castle becomes invaded by the resistance; flying in by Dragon riders and swift Pegasai: starting a brawl in the Castle's hall.
[#18] Commander Hurricane and his militia try to hold a steady wall to allow the rest to proceed further into the Castle.
[#19] Quin and Elgon stay behind to ensure the Timberwolves can't pass the hall's doors, leaving Twilight and Luna to head to the Main Chamber to confront Discord.
[#20] Luna is reminded of her impending entrapment on the Moon by the hands of her dear sister from Discord, trying to make her change sides.
[#21] Luna takes Twilight's words and goes to her sisters side, irritating Discord for being too soft as Twilight tries to keep Discord occupied.
[#22] Regardless of being unable to keep Discord away from Luna, the endangered Luna's tears was able to awaken Celestia and the sun brightly shines through the storm around the castle.
[#23] Luna apologizes and Celestia does too, creating the needed spark to correspond with the Gems, supplying enough magic to turn Discord into stone and provide a glow to push the shadows back into the Everfree Forest.
[#24] Discord's words lingered as the shadows faded- asking for Twilights name; stating to never forget him, as he'll never forget her and of her friends she spoke of.
[#25] Though things return to normal and Celestia and Luna agree to hold equal power, Luna still is nervous of her "Power of Night" and wanders off.
[#26] After receiving thanks from Celestia, Twilight finds Luna back at the meadow and comforts her.
[#27] Opening the mysterious parcel from the beginning, Twilight reveals the contents to be friendship bracelets; custom designed for all her friends she made since moving to Ponyville. She gives one to the young Luna.
[#28] After words of wisdom and hope for a better future, Twilight uses a unique magic charm spell taught earlier by Quin which allows one to meet with the other when in danger, no matter what.
[#29] With the exchange in gratitude, Twilight's bracelet glows at her again, passing her back to her own time- unable to hear each others last words.
[#30] Back in the Gallery of Ages, no time has passed, and the day continues as normal as Twilight goes to meet the others to give them their bracelets.
[#31] Twilight starts reading out a soon-to-be-written letter to both Princesses reading: "No matter where you are, friends are always closer than you think".
[#32] Luna and Celestia watch from the balcony above- Luna wears her bracelet as she attempts to remember events from the young unicorn from long-ago.
[#32] Luna is about to read her already planned reply; "See you soon". Close.

-Last Note-
Without further ado, I should actually start writing this semi-script up for you to read through, but we'll see how that goes.
I hope you like this "episode" and can see and hear the story itself when reading.