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

Unsettling dreams are starting to worry Princess Luna. She is positive these dreams hold an ominous portent for all of Equestria, but there is only one stallion who knows for certain the answers she seeks. King Sombra has been imprisoned again in Shadow since his defeat and the shattering of his body, but he is no less cunning and ruthless. And as Luna tries to interrogate him over time, she finds there is a softer side to the unicorn king, one nopony has seen before. But Celestia fears for her younger sister, warning Luna against Sombra's advances. Is the once-tyrant truly starting to court Princess Luna...or is she simply being used as a pawn in his plans to regain power?
~~~
Cover art by the amazing MickeyMonster, who has permitted me use of it for this fanfiction, as this image inspired me to write this story in the first place.
Edited and proofread by my girls TheOneBehindYou and LabyrinthineMind.

8tracks playlist: https://8tracks.com/yoru-the-rogue/lingering-shadows

Trixie is tired of being the cast-off and the laughing stock of Equestria. When she gets her hooves on a rare spell, she finally has the means to seek her revenge on Princess Twilight. Switching their bodies, Trixie becomes an overbearing royal overlord who wants everything her way. In the meantime, Twilight is stuck in Trixie's body and the Mane 6 have all been scrambled. Twilight and her friends have to find the answers to this puzzling spell before Trixie ruins Equestria for everypony!

[Prototype 2/MLP crossover]
After a number of years, Nightmare Moon has returned and was able to make her own body, instead of finding a host. However, the process cost her most of her power, and she knew that, if she were to get it back before being discovered, she needed to get herself a familiar.

However, things don't go quite as planned, as the ritual end up costing her wings, and she gets quite a willful familiar. Over the next few days, she is forced to admit that her ultimate wish is that ponies liked her night, and through that her, by forcing them to experience it. With this relevation, she is faced with a new goal of getting the ponies to like her, which will be a even harder task.

Luckily (or perhaps unluckily) her familiar is there to help, with his intimidating visage, abrasive personality, and willingness to brutalize anyone needed.

AN: This is my first time.

Also, it has been pointed out to me that I should probably get a Editor. So anyone willing, the position is open.

It has been one of the closest guarded secrets of Canterlot's royalty. Deep in a specially constructed dungeon, surrounded by warding spells and powerful magic barriers, exists an enigma. Within a cage that could only be described as something out of a nightmare, it waits and watches all of Equestria. A creature that cannot age, is immune to disease, does not thirst nor hunger, and resists all injury. But, it also holds secrets and knowledge that could safeguard the kingdom. Its powers are frightening, but it is civil enough for debate when patience permits.

Princess Celestia has sought counsel with the creature before, enduring it making deal after deal for its services. The Princess walks a fine line when dealing with it, knowing full well anything could give it an advantage despite its imprisonment. She has had to go back on her word in these dealings, and from this a deep animosity between them has been born. It is a necessary evil as she is convinced this is a being capable of untold evil far and above anything Equestria has ever dreamed of. So long as it remains within the confines of its cell, her kingdom is made safe. So much magic has been woven to ensure that, there is little chance of escape.

So long as the magic holds, there is no danger. So long as the cage remains strong, the nameless creature stays enthralled in his cavernous dwelling. If that were to change--if the magic failed--not even the wisest could say. But one thing is assured, it does not bode well for Equestria.

This story is a sequel to Becoming One With the Night

It was supposed to be a good day. Twilight and Luna were sharing the news of their relationship with their closest friends and family. However, Celestia's largest secret yet finally came out. Now, relations are strained between Celestia and everypony else. After all, what's Twilight to do when she finds out her second mother is actually her birth mother?

On top of this massive bombshell, soon Twilight will be sporting a pair of wings of her own. If she thought things were complicated now, just wait until Canterlot gets wind of a new alicorn. Life is about to become one giant nightmare for Twilight. But hey, at least she has Luna, right?

As stated above, this is a sequel. I highly encourage you to read the first story (the writing is extremely rough early on, mind you), but it's not entirely required to understand most everything that will be going on here.

EDIT: Takes place during S3, when it was originally conceived, thus the Alt. Universe tag. There was no redemption of Discord. There was no ascension. Yes, the Crystal Empire is back, and Cadance and Shining Armor are the leaders there. This should cover the more critical aspects of the season in regards to the story.

This story is a sequel to Celestia's Twilight

We all know the story. One thousand years ago Princess Celestia was forced to banish Nightmare Moon to the moon to save all of Equestria, but what if Luna had been hiding something from her sister, scared of how she would react? When Luna had no other choice, she cried out for Celestia and Celestia came. For one thousand years, Luna wondered what happened when Celestia left; now she's finding out...

But is it already too late, or will Luna be able to take the role she had so long dreamed of? The dream of being a mother?

editor Don't Look At My Name Bro! and RK I am lost without you!

Anon likes his life to be simple. He wakes up, goes to work and sometimes gets himself a good book to read while he is home. It's a routine that he likes to follow, it makes him feel like he has a bit of normality with his life in Equestria. The fact that having Celestia come crashing into his home as part of his routine should prove that his life is anything but normal.

(Thanks to PeerImagination for editing!)

Presenting Princess Celestia, fair and beloved ruler of Equestria, and her daughters, Luna and Twilight, heirs to the Equestrian throne.

Wait, what was that last bit?

Due to an unknown spell, Princess Celestia must take care of her new young daughters as she fights her stronger-than-ever motherly instincts while finding a way to return everything back to normal.

Now with 20% more cover image thanks to the wonderful LevelDasher!!

FEATURED BEYBAH!
03/23/15-10/16/15
It was featured again while cancelled lol (19/10/20)
Thank you, everyone!
This was adopted from TheFaceOfMercy

Finding herself with wings and unusually powerful magic, Twilight Sparkle proceeds to have breakdown after breakdown, until with the help of her friends, she confronts Celestia and Luna about it... And learns that she's a far more important little pony than she ever imagined - for all the wrong reasons.

Awesome painting by Drezzer can be found here!

20 megapixel version is here (10MB JPEG, 210dpi strangely, 24"x20")!

Thanks, man!