This story is a sequel to Princess Celestia: A Brief History

  When Celestia first laid eyes on Twilight Sparkle, she knew she’d seen her somewhere before. Though she’d managed to hide this from both Sunset and Twilight, after they departed for the evening, Celestia needed to be sure.
  With her trusted aide Raven at her side and a dangerous threat on the horizon, Celestia heads to the offices of the Equestrian Secret Service to investigate her suspicions.
  Because if she’s right, the possibility of eternal night is the least of Equestria’s concerns.

In FimFiction's Feature Box from October 17 to October 21, 2016 with a Hot tag!

Featured on Equestria Daily on October 23, 2016!

Historian’s Note:
In a timeline where the Sonic Rainboom didn’t happen, The Cloudsdale Report occurs directly after the events chronicled in Princess Celestia: A Brief History, which occur the day after The Application of Unified Harmony Magics.

Cast: Princess Celestia, Raven, Philomena, Twilight Sparkle, Sunset Shimmer

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 Design by Amber Spark in Pixelmator
Celestia’s Cutie Mark by BlackGryp0n (Yes, that BlackGryp0n)

Beta Reader Credits
Ebon Quill - Quest Designer on The Manehattan Project
Little Tinker - Master of Systems at Ponyville Live & Scripting Engineer on The Manehattan Project

This story is a sequel to The Application of Unified Harmony Magics

  After the incredibly awkward reunion last night, Sunset is less than eager about her promise to introduce Twilight Sparkle to Princess Celestia. Maybe it would help if Twilight could go more than five minutes without a panic-driven ramble.
  Despite her doubts, Sunset decides to do her best. But between a bowl of ice water, Philomena’s antics and Celestia’s sly smile, Sunset knows this isn’t going to be easy.
  Still, Twilight probably could have handled it better.

Featured as a Sequel on Equestria Daily on October 8, 2016!
Appeared in the FimFiction Featured Box on September 27, 2016!

Historian’s Note: Set in the Wavelengths timeline where the Sonic Rainboom didn’t happen, the events of Princess Celestia: A Brief History occur the day after the story The Applications of Unified Harmony Magics.

Cast: Sunset Shimmer, Twilight Sparkle, Princess Celestia, Minuette & Philomena

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 using Pixelmator
Princess Celestia Vector by Wrathx79
Princess Celestia's Room by tamalesyatole
Sunset Shimmer Cutie Mark by MillennialDan
MLP Book Vector by SnowedEarth
MLP Magic Aura Vector by AimeeLovesU

Beta Reader Credits
Ebon Quill - Worldbuilding Writer on The Manehattan Project
Little Tinker - Master of Systems at Ponyville Live & Scripting Engineer on The Manehattan Project

Special Thanks
Fahrenheit - For wonderful advice on creating an epic and entertaining synopsis!

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.

As the Princess of Friendship, the only thing Twilight Sparkle loves as much as books, reading, books, making new friends, books, spending time with her friends, and...books...

...is spreading the magic of friendship. And one easy way to do that is to introduce your friends to each other.

In need of a weekend away from the castle before heading out to the Crystal Empire to spend time with her family, Twilight decides to take a little vacation to the human world...and brings three of her newest friends along.

After all, if Princess Ember, Moondancer, and Starlight Glimmer are all Twilight's friends, surely they'll get along well with each other and with Sunset Shimmer!

Right?

(Cover compiled from various source vectors.)

Luna discovers a lone member of the Royal Night Guard stationed beneath her private balcony. As a question becomes a conversation, as an evening becomes a week, and as an annoyance becomes a friendship, an unfortunate truth looms large in her mind: nothing is ever as it seems, neither in dreams nor reality.

Comments contain spoilers
Edited by PresentPerfect and Grand Moff Pony

When some of her friends develop a relationship after spending a few days out to solve a friendship problem, without finding any friendship problem in the first place, Twilight Sparkle start to think something is wrong with the Cutie Map. She's mostly right.
Warning: Story is very silly and we can only hope it never turns out to be canon.
Rated T for some sexual references.
Proofread by the awesome Nephox Venom.
EDIT: Featured in 18/10/2016! YAY! THANKS GUYS!

While hanging out with her friends, Sunset Shimmer learns that earth horses apparently can't vomit.

As a magical talking pony, this discovery utterly baffles her.

Proofread by the ever helpful RQK

Tirek had returned and this time there was nothing that could be done to stop him. The Elements of Harmony had been defeated, the Tree of Harmony had been ripped from the ground, and every spell that was thrown at Tirek was useless. It was only a matter of time before he found the alicorns and then all would be lost.

What happened next though, nopony saw coming.

Now with a Russian translation, which can be found here.
Big thanks to Armorer.

It's official. Twilight Sparkle is dead.

Better luck next time, I guess.

She really, really is.

And Twilight has to deal with it.