This story is a sequel to What I've Become

It is highly recommended that you read What I've Become before you read this story, since this is the second story in The Humanity Within Trilogy, and you will be lost if you just plunge into this without any preparation.

Also, this story already has a sequel: What I Am!

Things have been turning up roses for me lately. I'm no longer fighting to survive, I have people that I can turn to, and I have my face back, all because of the kindness shown to me by strangers.
But will they continue to help me once they find out what dark secrets haunt my past? Will they shun me for the evil deeds that my abductors forced me to do while I was in their service? Will they continue to protect me from the monsters that destroyed my life, once they realize what kind of monster I really am?
How does one forgive a murderer?
WOOT! Feature the day it came out! (how did that happen?) 12/1/2014
Edited by Malefactory. He is fantastic at this kind of thing!
Proofread by Cantankerous. He's freaking amazing.
Also proofread by PhiliChez.
Cover Image done by the very talented PaintSplotch! You can find his FimFic account here.
And here is his DeviantArt Account!

This story is a sequel to How Not To Use Your Royal Prerogative

  In an Equestria where the Sonic Rainboom never happened, Sunset Shimmer is the prized pupil of the Princess of the Sun. As Sunset struggles to make up for her past misdeeds and come to terms with the pony she wants to be, Celestia sends her to find the classic work The Application of Unified Harmony Magic from the Royal Canterlot Archives.
  Right after lunch, some meddling by her friends and meeting somepony with firsthoof experience of the Sunset she used to be.

Featured on Equestria Daily on August 18, 2016!
Appeared in the FimFiction Featured Box!

Cast: Sunset Shimmer, Moon Dancer, Minuette, Twilight Sparkle & Princess Celestia

Stories set in the Wavelengths Timeline in chronological order:

Origins Arc
The Alchemy of Chemistry
Bards of the Badlands
Grading on a Bell Curve
Habits of the Equestrian Phoenix
How Not To Use Your Royal Prerogative

Applications Arc
The Application of Unified Harmony Magics
Princess Celestia: A Brief History
The Cloudsdale Report

Dreamers Arc
Tactics of Snowbound Unicorns
A Study in Chaos Theory
Teahouses of Saddle Arabia
As the Raven Flies

Cover Credits
Cover Design by Amber Spark
Sunset Shimmer Vector by TigerBeetle
Pony SciTwi Vector by Osipush
Canterlot Bookshelves Vector by FavoriteArtMan
Sunset Shimmer Cutie Mark by MillennialDan

Beta Reader Credits
Ebon Quill - Worldbuilding Writer on The Manehattan Project
Quantum State - Technical Director of The Manehattan Project
The Albinocorn - Master of Sunset Shimmer Stories

Strongly Recommended Stories:
The Brightest and the Best by Pineta - The events in this story are considered to be completely canon to this timeline and explain Twilight's entrance exam to Celestia's School for Gifted Unicorns. I cannot recommend this story enough.
MLP Annual 2013 - "The Fall of Sunset Shimmer" - As above, the 8-page short comic in the beginning of the Annual is also considered to be canon, though with some major variations.

Version 3.0 Edit: Extensive grammatical and mechanics changes. Adjustment to timeline of Sunset's second mirror experience.

Though most view them as simply immortal powerful rulers, some ponies worship the Princesses as actual Goddesses. Some families with deep Earth Pony roots worship the old Nature Spirits of their ancestors.
But some ponies turn to darker forces. They worship monsters and demons, praying for plagues and misfortunes upon those they despise.

One day, Discord finds out that in his "extended absence", a cult formed with him as the Central Deity. Unfortunately, it's not exactly what he would want. These ponies will soon find out it's a bad idea to anger your god.

Edit 5/18/18: New cover art courtesy of the illustrious Mix-up. Check out the original here.

Garble has won the Gauntlet of Fire and taken the Bloodstone Scepter. Upon hearing of this, Celestia, determined to stop the bloodthirsty Dragon Lord in his tracks, challenges him to a one-on-one duel for the fate of Equestria and the Dragonlands. An immortal alicorn capable of moving the sun with millennia of experience under her belt versus a teenaged dragon with no experience at all.

Garble accepts.

Stupider things have probably happened, but it's hard to say how.

Cover art is taken from this comic by Niban-Destikim.

My name is Aedan and I'm your average run-of-the-mill guy from Missouri. I served in the Marine Corps for about four years, now I've been out for a year and I'm making a living on the edge of St. Louis. It's not the best of conditions for a guy like me to have to deal with, but I adapt and overcome. Then one Saturday morning on my daily jog I ran into something (well in truth she ran into me) I'd never thought possible. She calls herself 'Princess Luna'. She's alone and confused, but most of all, she wants to go home. And guess who the poor guy is that decided to help her.

rated Teen for talking like a Marine and some... 'Adult' situations...

When I first met Princess Twilight, she was confused, lost. Adrift in an alien world. I thought of her as a rich eccentric, certainly a foreigner. I humored her as much as I believed her, really. Even when she dragged me to the very ends of the world in her mad quest for a mythic well, I really did it all for her. I figured it would help her find some closure, and we could go home.

I was right, in a way.

Based roughly on the game 80 Days.

[ Inspired off Season 5 Finale - Nightmare Moon Verse ]
Social reject, blank flank, and failed candidate for Celestia's School for Gifted Unicorns, Twilight Sparkle's life couldn't get anymore depressing even if she tried. Yet still she looks to the other things in her life to get by, such as her job selling donuts at Joe's Bakery, her best friend Smarty Pants, as well as her inspiration to someday be as great as The Great and Powerful Trixie herself! Life isn't as bad as it may seem, and she enjoys the simplicity of her daily routine, the peace of her recluse world. That is until suddenly she is targeted by the current ruling body of Equestria, Nightmare Moon herself!? Perhaps she spoke too soon. Better run Twilight, destiny is calling!

On the Day of the Dying Sun, she performed Astrum Nova. From then on, that world ceased to exist.

Twilight Sparkle, daughter of the highly exalted Captain Night Light, was (to put it lightly) hilariously underwhelming. The only reason why she was one of Princess Celestia's students? Because a place as a personal student of the princess was a reward for the captain. Other than that, she was a scrawny unicorn with no actual magical talent, other than the whole bunch of magical theories crammed into her head. To make it worse, Sunset Shimmer, greatest unicorn the world has ever seen, was her only classmate. But Celestia has entrusted her with a journal, and the knowledge of the Elements of Harmony and the harmonic energy field they radiate, keeping Equestria safe from harm for eons. As a sinister plan for a coup emerges in Canterlot, Twilight must find and gather the Elements and their bearers. But how is this possible, in a world where castes and tribes separate true friendship? In this story, Twilight must discover new friends as she uncovers dark truths and questions about the events leading up to the present-day Equestria. Who was Starlight Glimmer? What was Astrum Nova? And most importantly, how is it possible that the journal was written by another (and for some reason, winged) Twilight?

***FEATURED 25/5/2016***
Credits for cover art here

Warnings: Sporadic updates, long/plodding, backstory shipping

When Spike went to bed, he was a 162 year old dragon, war veteran, twice widower, and living on the outskirts of Ponyville. This morning, he wakes up to a voice he hadn't heard in decades on the eve of the 1000th Summer Sun Celebration.

Now, Spike must choose between the future he knows and a future he can make.

Sunset Shimmer has just graduated from Canterlot High School, and while that would normally be cause for celebration, it fills her only with a nameless dread as her friends begin to scatter to the winds to pursue their futures. With the latent magic of the human world contained and categorized and the Rainboom's idyllic days of schoolwork over, she finds herself without aim and listless, as though something important is missing from her life.

Fortunately for her, Princess Twilight Sparkle might know what ails her.
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So. First time posting on the site after a VERY long period of lurking and reading and enjoying the tales this fandom can produce. To my surprise, I found a dearth of a certain subset of story that I wanted to read, and so I have done this, to put my thoughts to words. After all, it is said that one should write the story they want to read, yes? I've been inspired by a variety of stories like it that came before, and I hope to equal their quality.

I'll try to update roughly once every couple of weeks; please be patient with me and I hope you give this tale a once-over. Pre-emptively tagging with AU, that I might diverge freely from what may come if needed.