There are only two ponies not joining in on Rainbow's break down. One's a stoic, so the reason is obvious. But what about the Princess of Friendship? Isn't empathy in her job description? And not a single tear.
From Season 5 Episode 5, "Tanks for the Memories."

Inspired from Crying on The Inside By Arwhale.

Yes, I know it's late. As always, your criticism and praise is welcome in equal measure. I do mention shipping, but I think you'll quite like it.
There's also a tiny bit of swearing because in my head canon Twilight would use it for the sake of hyperbole.

I have a video review! Yes, I did watch it, Yes, I know it says don't read it, and frankly you should listen to him! YouTube
Frankly I'm surprised anybody thinks this is good. As mentioned in a tiny blog blurb, I don't plan on revisiting this story because I have other terrible crap to write. I'm sorry for subjecting the internet to this.
But if you think this is bad, just be grateful I don't publish the droll I wrote in High School.

Failing once in her attempt to take Canterlot and failing again in her attempt to take down Twilight, one would think Chrysalis would have cut her losses and let things be, but the queen has once again appeared, this time in broad daylight with no disguise and no army. Her weapon of choice? Diplomacy.

Now Twilight is having to deal with the changeling queen, but surely putting up with her antics will be worth the knowledge she's willing to provide about her mysterious race and the potential undiscovered agents still within their midst...right?

Takes place before Magical Mystery Cure and diverges from there.

With thanks to MisterGunpowder for proofreading and editing.

Revision History:

05/09/2015: Chapter 1 updated with millions of little corrections.
05/20/2015: Chapter 2 revised and edited with another million small and large corrections.
06/12/2015: Chapter 3 given a thorough editing and revision.
06/23/2015: Chapter 4 taken to the gutter and edited twice to be sure.
07/14/2015: Chapter 5 thoroughly brutalized with the editing stick.
08/03/2016: Chapter 6 finally edited. Yes, I'm still alive, dammit.
09/29/2016: Chapter 7 fell out of the editing tree and hit every editing branch on the way down.
10/26/2016: Chapter 8 has emerged from the editing emergency room.
11/17/2016: Chapter 9 found and edited. No casualties reported.
11/30/2016: Chapter 10 treated for whiplash after lightning fast editing.
12/22/2016: Chapter 11 edited. Chrysalis shot first.
01/17/2017: Epilogue edited. Time to hit the cider.

A brave stallion goes on a quest to save the world by finding a lost princess in an enchanted forest. Things don't work out as he planned.

WARNING: Some spoilers in the comments. Also, a few mild spoilers for the Alicorn Adventure series, though it's not necessary to read those stories to understand this one.

Equestria Daily Page
Goodreads Page
Zabaware/AT&T Natural Voices "reading" by Modoc

Twilight, my Faithful Student, my friend, if there is anypony that can create a world of Harmony, true Harmony, it is you.

More than a thousand years ago, my sister and I sought to create a perfect world, a world ruled by Harmony. A world free of evil. We were powerful and believed ourselves above the laws that governed this world. But this world is governed by the laws of Magic, and Magic, it seems, demands balance.

Where there is Light, there is Darkness.
Where there is Order, there is Chaos.
For there to be Love, there must be Hate.
For every Dream, there is a Nightmare.
Each begets the other.

And like boiling water over a fire, each can extinguish the other.

I should not have been surprised when the day came that the evil I had to fight was my own sister. It was the world restoring the balance we so foalishly ignored.

Perhaps, it is for this balance that I now stay my hoof. I have chosen to have you,Twilight Sparkle, act in my stead as the evils I thought vanquished, inevitably return to Equestria. It is in hopes that you may learn this balance, that you may learn from my mistakes. It is not something I alone can teach you, when I myself still understand so little. It is why I must now rely on the help of an old nemesis.

He intends to take you away, my protégé, and make you his own. You must not succumb to his influence. Yet if you are to learn the balance that is at the essences of all things, it will be through him. For the future of Equestria and for the sake of Friendship, you must prevail.

I hope that some day you can forgive me.

Luna, sister to Princess Celestia, and Princess of the Moon, has been hiding a secret that she has kept from everypony, even long before she had been transformed into Nightmare Moon...

She has been killing ponies while they slept, taking their souls to who knows where...

What thoughts in her mind have clouded her sanity, and driven her to do what all ponies consider to be the most heinous and unforgivable crime in all of Equestria? What happens when she takes a loved one far too soon before their time, and her horrible secret is brought to light?

On a patrol through the White Tail woods, Twilight comes across a dying changeling. Torn between giving up the drone to the guards or leaving it in the inhospitable wilds, Twilight reluctantly takes the drone in. As it awakens she realises that the drone was a blank slate, with no connection, no 'programming' guiding its functions. So Twilight sets out to teach this changeling about the world, one hoof step at a time.

Rated Teen for slightly mature themes involving ethical dilemmas.

If Word Worthy stopped editing for me, I'd likely wind up as a grammar-less hack. Thank you, thank you, thank you!

This stories is redone and continued in: The Student of Sun and Shadow

King Sombra's attempt to reconquer the Crystal Empire may have been thwarted, and he himself cast back into the shadows, but it will take more that that to stop a being who endured a 1000 year of imprisonment in ice and darkness. Especially now that he has set his sights on a new conquest. Twilight Sparkle's effort to save the Crystal Empire may have gone unrecognized, but not by Sombra. She has earned his interest, and his admiration. The implications of which Twilight fails to appreciate. And will regret.

This story was inspired by the fan comic A Somber Meeting by Omny87

The Witch of the Everfree... a tale that has spread among all who live by the ever illustrious forest, to whom the witch truly is, no one knows apart from the one herself... until now. Twilight Sparkle had lived in the Everfree throughout most of her long life, since the corruption she was alone until not long ago when she met few companions. Trained along side her sisters through bond in arcane magic, given true immortality, she continued her studies alone only every now and again seeing how her race fared. Now, forty years after she was dubbed a witch by her race, three little girls stumble through her woods in search of the ever mysterious "witch", what could really happen? read to find out.

FEATURED: 16/03/14

Clarifications:
Many have wondered what Twilight looks like and such so to clarify, she does not look like a human female, she retains her fur coat, she is of human height and has hands. The facial structure is more detailed such as where the eyebrows should be there is a darker patch of coat much in the color of her mane.

The story starts a few episodes in, around halfway through season one I would say, some shall stay canon whilst some with alter, I am sorry for this inconvenience.

Twilight is still Twilight in every way, though she has been with little to no contact throughout her life apart from when the Everfree retained people, in such her words would become haggard sometimes so that's why you will probably go "huh" when you first see her talk to the CMC.

That is all for now.

Today is Princess Twilight Sparkle’s 500th birthday, and her most faithful student, an earth pony with a familiar name, can’t wait to celebrate!

Notes:
- Cover art by ErinKarsath, used with permission. Check out her DeviantArt page.
- This is a story in the Birthdayverse, and you can find the sequel here.
- Many thanks to my faithful Pre-Reader and all around super-duper best pony, Blood Lord. Go read his story, too!
- This was written during the season 3 hiatus of MLP:FiM.

Twilight was supposed to gather the Elements of Harmony the way Princess Celestia planned it: meet the embodiments of the Elements while running errands in Ponyville, team up with them, discover the meaning of friendship, and then defeat Nightmare Moon. It was all so simple.

Too bad she really underestimated Twilight's ability to screw things up.

Additional Character Tags: Octavia, Nightmare Moon, Princess Celestia, Shining Armor, Princess Cadance

Edited by WorkbenchManiac: chapter 7-25, 27 onwards
Edited by docontra: chapter 26 onwards