There are few things more potent than being told “You can't.” For some, it's the most destructive thing you could ever say, and could drive them to give up everything they've worked for; for others, it serves to inspire their ultimate effort in order to prove them wrong, even if they're hopelessly outmatched and seem to have no hope in Hades at meeting their challenge. This is the crossroad Twilight faced when she was told, “You can't beat me no way, no how,” inspiring her to train until she felt ready to face someone who could knock her out in one punch. As she gives her all to preparing for her bout in Las Pegasus, the one thought running through her mind is “Her hits make apples fall from trees! How in Equestria can I beat that!?”

Mis-communication has started many a war, but in this case maybe calling it a war was too generous.

The "war" is over, Twilight has successfully orchestrated a bloodless end to the Griffons' aggression, but only now does she realize that there is more to winning than she had first assumed, especially against a nation that holds war as a central part of their culture...

Now Twilight must deal with the aftermath while facing a challenge she never anticipated: being seen as a conqueror.

This can be read alone, but I recommend reading the letter that started it all for a chuckle and a little exposition. This series of expositional one-shots can also give some additional world-building.

For a thousand years, the Code of Harmony has ruled Equestria, and the Code of Dissonance has sabotaged its works at every turn. Now the war for control over the land will come to a head, and one unicorn's decision may decide the fate of all.

For though she does not know it, Twilight Sparkle is the shining example of the Code of Harmony. Her teacher, Princess Celestia is Harmony's most powerful master and she knows her enemies are hatching a plan that threatens to cast down the Harmony of her throne and all she has sacrificed to create.

What she does not know is her foe seeks a new Apprentice to turn to his dark ways. A unicorn with seemingly limitless potential for magic, whose thirst for knowledge may yet lead her down a dark path, who is known to be such a faithful student of magic, eagerly seeking the truth no matter how forbidden it might be...

Sequel: Code of Harmony

This story is a sequel to Rot

After the events in 'Rot', Twilight Sparkle has finally come to terms with her new self. Can she control her new powers? Can she ever have anything close to a 'normal' life again? And what happens when Discord's past mistakes come home to pass judgement on the 'new' Princess of Friendship?

Twilight Sparkle has always been frustrated with Discord. His ability to do anything, with no more effort than a snap of his claw. It shouldn't be possible. His power had to come from somewhere.
Then, one day, Twilight lets slip how she feels. Surprisingly Discord agrees to explain it to her. To give her the secret to all of his powers. If she's willing to pay the price that knowing it all will bring.

WARNING: Sequel to 'Then Tomorrow Came'. Spoilers ahead.

Through great hardships and heartbreaks, Twilight Sparkle has finally "won" the heart of her beloved Rainbow Dash. But will she have the chance to finally enjoy the peace and happiness of her hard won victory? Will the consequences of her extreme actions catch up with her? And what will happen if Rainbow Dash ever begins to suspect the truth?

Rated T for language, implicit sexual content, and morally confusing arguments regarding neuroethics. Again, this is a sequel to Then Tomorrow Came. If you haven't read that, this isn't going to make much sense.

Twilight never cared much for romance, but after falling for Rainbow Dash, she's ready to make her move. But what happens if those feelings are unrequited? Should she hold onto hope? Is it even possible to let go and move on?

I've read a bunch of shipfics that are all happy resolutions after the confession so I wanted to try an alternative. So here is a slightly darker TwiDash fic because I am a terrible person who must make ponies suffer. Oh God Why?!

Edit: Now with addition of new cover pic used with permissions from aeroytechyon_x
Reformatted with less walls of texts and less Lavender Unicorn Syndrome as of 03/20/2015

Sequel here.

This story is a sequel to Emerald Gleaner: Retired Monster

[Prototype 2] X MLP:FiM Crossover

Beset by a mountains of work both official and secret, Emerald has barely time left to herself anymore. Can one still become exhausted even if they physically can't? When does paranoia do more harm than good?

When people stop trying to kill you of course!

Be Awed and Amazed by the tale of Sweetie Belle as she traverses the multiverse in search of her lost mentor and friend, Twilight Sparkle! Will she find her in post-apocalyptic Equestria? Or maybe in a strange world where everypony is the wrong gender? Or even where a Pony claims to be a human? Read as she journeys through very familiar worlds you might have read about... if you dare!

At this point in time all the main worlds to be visited have already been chosen. Thank you all for the suggestions, and I hope you enjoy the surprises!

Here's the official TSC:F Music Intro: The Sweetie Chronicles: Fragments

WDTP: S2/3-CE
You can also visit the TV Tropes Page which has spoilers!

This story is a sequel to Oskar Osäker: True Omnivore

[PROTOTYPE 2] My Little Pony: Friendship is Magic Crossover

Oskar's secret has been revealed to Twilight in totality, now Twilight faces the moral quandary of betraying her friend or betraying her morals. The events of season 2 are fast approaching as well and the ripples Oskar has caused through his mere presences alone changes more and more. Can a friendship survive when one of the friends is a murderer?

Thanks goes to: NightmareKnight for spending time being my editor, Trondason being an all around great fellow and helping me with ideas