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.

Twilight is almost used to being an alicorn now. She's accepted that unexpected change, and is even happy about it, most of the time. Her magical abilities have grown by leaps and bounds, and she's starting to enjoy the freedom offered by flight. While she can't imagine ever being as good as Rainbow Dash, anypony with reasonable standards would by now consider her quite competent in the air.

But despite her growing enthusiasm and confidence, there's something that she has neglected to deal with. Something that's bothered her at times ever since the transformation, but kept getting shuffled down her list of priorities. Fortunately, she knows just the pony to talk to for help, and she won't let nervousness and self-reliant rationalization hold her back anymore. The latest of Pinkie Pie's parties provides a perfect pretext for a conversation she should've had months ago.

If you're confused by the date listed on the chapter, that's just when I originally uploaded it for pre-reader viewing. Life got in the way and I didn't get around to hitting Submit until Feb. 7, 2016.

There is a giant hole in the wall of Twilight's castle. Most of her front door is gone. And Rainbow Dash had better have a good explanation for this.

Top ten finalist for the "Look, I can explain" writeoff.

After finding Discord hiding out in his closet, Twilight Sparkle soon learns the most horrible of truths about herself and the world surrounding her.

And then she learns another truth.

And another. And another. And...

Twilight Sparkle is seven years old, and she already knows a lot about the world. What she doesn't understand is her mother: Why does she work so hard when she could be home with her family? Her teacher, Princess Celestia, explains it as best she can.

Twilight has a brand new theory. She has theorized that it is possible to create pocket dimensions and a way to enter them. Facing the ridicule of the rest of the theoretical magic community she has set forth to prove them wrong. She will construct a portal and enter it.

She does. Inside, she finds a field of empty white.

The story now has a dramatic reading by MrSnarky. Visit his channel on youtube.

During her time-twisting battle with Starlight Glimmer, Twilight finds herself in an Equestria ruled by a tyrant alicorn that calls herself the Queen of Equestria. In this world, Twilight's friends are gone and beyond her aid, and Equestria's citizens live in fear of their ruler's wrath should they anger her.

But no one has ever seen the pony who suffers the most in this world.

Pre-read by MythrilMoth and RT Stephens. Cover art vector by kindkristy99

Every morning, Princess Celestia wakes up in terrible pain, and every morning, she chooses to endure it. Until one blissful day grants her the blessing of feeling normal.

Few things in her life have ever frightened her so much.

6th-place winner in the /fic/ write-off "Look, I Can Explain..."

Featured on Equestria Daily!

Reading by Skijaramaz

Now translated into Russian.

When one's genetic template is overwritten, there tend to be... side effects. Most of the side effects come into play immediately.

Sometimes, though, one has to live with a new biochemistry for a while before it triggers.

It's actually very well documented.

Written for FTP13. Cover art by cheezedoodle96.

Starlight returns from the marketplace to come across two sworn foes calmly sharing tea, much to her confusion.

Much to her confusion.