Warning: Wall O' Text!
This is an idea of what is inside the box (aka "The Ark") that is at the base of the Tree of Harmony.
Starswirl the Bearded is revealed as being the mystery pony seen at the end of Castle Mane-ia. He makes several appearances during Season 4, constantly drip-dropping innuendo about Celestia's past and whether she is really worthy of Twilight's love and admiration. Celestia, when asked by Twilight, is... vague... even openly evasive about Starswirl's charges and, when they confront each other, there are real sparks between them even though there is also clearly a bond of great love between him, Celestia and Luna.
Finally, when the Ark is opened, a rainbow vortex appears, leading into the box (say it with me, my little ponies: "It's bigger on the inside"). Starswirl starts raving about 'the wellspring of Harmony' and 'undoing a great mistake' and throws himself into the vortex. Without a second thought, Twilight throws herself after the clearly-insane wizard in an attempt to prevent him from harming anypony (even himself).
As she plunges down the rainbow tunnel, Twilight sees events from Celestia's past:
A very young pegasus Celestia rearing up to drive off a Manticore as a group of ponies cower behind a unicorn Luna and an unidentified male earth pony.
An adolescent alicorn Celestia falling from the sky, her wings singed as a monstrous dragon soars overhead
A young adult unicorn Celestia levitating a sword in her magic and duelling with a Changeling Queen who has a sword of her own...
An adult alicorn Celestia (still pink-maned), standing next to a blue-grey maned alicorn Luna and the Unidentified Stallion (now an alicorn) as they face a cackling Discord
Twilight lands hard on all four legs and looks around herself frantically. She is on a barren, rocky plain with tall rocks all around her. Seeing any distance is nearly impossible due ot thick fog.
Hello? Princess? Anypony?
There is a clatter of hooves; Twilight spins just in time to see a white Pegasi with a pink mane and tail and a sun cutie mark rush by.
There is a motion behind her. Twilight spins and we see an older, pink-maned alicorn version of Celestia , appearing briefly through the fog as she strides determinedly somewhere.
Twilight staggers and falls to her knees. She begins to cry
I don't know where I am!
Twilight! Twilight Sparkle, can you hear me?
Yes, Princess! I hear you! Where are you?
Twilight whirls as a adolescent unicorn version of Celestia in golden armour gallops past.
I can hear so many voices...!
Those are my ghosts... My pasts and futures. My every good day and my every bad day.
There is a scream from somewhere off-screen.
I... I feel so weak!
It is not given to any being to intrude into the very core of another pony's being in this manner, Twilight Sparkle, even one as wise and as powerful as you!
I can't find my way out!
It is simple enough. Take this flower.
A rose spirals down from the sky and Twilight grabs it in her magic and puts it in her mane.
Everything that you were, are and ever will be is represented in this simple blossom, Twilight. Take this. Hold it and never let it go.
Celestia, in her full, aura-maned alicorn glory steps out of the fog.
Now, I will guide you home.
Do not fear, Twilight Sparkle. I am not an illusion or one of the echos of past, present and future than inhabits this place. You have done so much for me, my most beloved and faithful student. You have saved me in so many times, places and ways. Now, I ask you to do the one thing that I have never given you reason to do: to put your trust in me. Allow me to save you as you have so often saved me!
Twilight staggers forwards and takes Celestia in a tight hug.
Oh my brave little filly; it's going to be okay.
Celestia suddenly freezes, her face a mask of horror as she looks at something behind Twilight
Seemingly partly recovered, Twilight looks around herself. Suddenly she sees something, a shadowy figure in the fog.
Look away, My Little Pony
But who is that, Princess?
Me. There's only me here, Twilight Sparkle, that is the point. But this is somepony that I pray you never come to know.
Twilight takes a step away from Celestia. The fog is thinner now; the figure is shadowed but humanoid, looking out from the top of a cliff at something.
I've seen all of you! So many faces and lives but they were all you. This one... I've never seen before! A human! You must have been through the Mirror too! Princess Celestia, why didn't you tell me that...?
Twilight is about to step forwards but Celestia's wing blocks her way and her view.
I said that she was 'me', Twilight Sparkle, but I never said that she was 'Princess Celestia'.
I don't understand!
Twilight ducks under Celestia wing. We see that the figure is standing amongst what are unmistakably grave-stones. The cliff on which they are standing is overlooking a plain that stretches away as far as the eye can see; it is marked with literally uncountable grave-stones. Twilight gasps.
Celestia uses her magic to yank Twilight's head around so she is looking at her again.
Twilight, what does my name mean?
It's in the old, ancient tongue; it means 'The Bringer of Light'
My name; Twilight, Starswirl was right to say that Celestia is not my original name but that isn't the point. The point is that the name with which I was born doesn't matter. When you choose a name for yourself, you're making a promise - a solemn vow to live in accord with the meaning of that name! I am Celestia, the Bringer of Light. My purpose is to make things better for all of My Little Ponies.
Celestia looks at the figure again, her expression haunted.
Celestia visibly swallows her disgust and sorrow.
She is the one who broke that promise. She is the one who has no right to bear the name that claims such a high purpose.
Twilight groans and suddenly collapses. Celestia effortlessly tosses the younger alicorn onto her back.
She is my secret. She is my shame.
What I did, I did without choice.
In the name of sanity, peace, Harmony, and all my Little Ponies.
Celestia's face hardens
Yes... but not in the name of Celestia.
The figure turns around and we see it is young human woman, wearing a khaki trench-coat. Underneath, she is wearing shining chain-mail overlaid with gold and silver plate armour marked with Celestia's cutie mark. She has long blonde hair, tied back with a red bow, and sad cornflower-blue eyes. Around her neck is a gold-framed heart-shaped locket on a golden chain. The locket's front is a rainbow-coloured crystal.
I've been running all my lives.
A young peagsus filly Celestia is looking on in horror as Tirek the Abomination blasts Queen Majesty with his full dark might
Running across the face of this world for tens of centuries; from face to face and life to life.
An adolescent alicorn Celestia, her wings and mane burning and her face frozen in fear, pain and horror, falls from the sky as a giant dragon flies overhead The POV rises up, through a corridor in a wall we see a pink-maned alicorn Celestia glaring determinedly out at something.
I've been running every second of every minute of every day for four and a half thousand years. I've resisted chaos, toppled tyrants and fought for peace in a world defined by strife.
The POV sweeps up and across a tableaux of ponies, past and present, including re-imagined ponies from G1, the Mane Six and hundreds of tumbling artefacts; Twilight Sparkle stands, looking into a crystal ball at an image of a unicorn Celestia duelling with a Changeline Queen, both using telekinetically held swords.
Now the time has come to face the consequences of all the choices I've made in the name of Harmony.
Harmony...! The Elements! Harmony...!
The future of Equestria now rests on the outcome of one moment of one single, impossible day.
POV leaps forwards past the figures of Celestia, Luna, Starswirl and Discord. The air is filled with tumbling artefacts including Celestia's royal vestments, both versions of the Elements of Harmony and various types of pony weapons.
The day that I've been running from for so long that I've forgotten what is is like not to be running.
Amongst the tumbling artefacts is a diamond-edged longsword with Celestia cutie mark in the centre of the cross-guard. A human hand reaches up and seizes the hilt
Megan rests the Sun Sword on her shoulder and smirks at the camera in a bitter, self-loathing manner.
The Day of the Alicorn.
Megan raises the sword to the skies and solar flame blazes along the length of its blade.
Begin Infinate Zoom Upwards
Standing behind Megan are an older Molly and Danny, who are both drawing their own weapons. Molly's armour marked with Luna's cutie mark and Danny's with Starswirl's cutie mark.
Behind the three humans are an army of hundreds of thousands of armoured ponies and fantastic engines of war including floating war machines and mighty land-crawling weapons platforms.
The Army charges just before the POV shoots into the clouds.
To be concluded in...
My Little Pony
The Day of the Alicorn
#Seizetheday - www.mlpdayofthealicornmovie.com
End credits to an instrumental version of "This is the Day"