Twilight was supposed to gather the Elements of Harmony the way Princess Celestia planned it: meet the embodiments of the Elements while running errands in Ponyville, team up with them, discover the meaning of friendship, and then defeat Nightmare Moon. It was all so simple.

Too bad she really underestimated Twilight's ability to screw things up.

Additional Character Tags: Octavia, Nightmare Moon, Princess Celestia, Shining Armor, Princess Cadance

Edited by WorkbenchManiac: chapter 7-25, 27 onwards
Edited by docontra: chapter 26 onwards

This story is a sequel to Friendship is Grievous

The brutal Clone Wars have at last come to an end. The Separatists are no more, and from the ashes of the Galactic Republic, the Galactic Empire has emerged. Now, the ponies of Equestria must choose their path through a dark and terrible time.

TV Tropes page.

Cover art by Mix-up over at his his deviantart.

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.

In the magical land of Equestria, two alicorn sisters raise the Sun and the Moon every day to give the world a night and day cycle, basic for the survival of life. There are also two alicorns who rule over two very core aspects of life and harmony itself. Those are Love and Friendship. While not as ancient as the two sisters, all princesses are essential to the world's balance.
This balance is also sustained by the hard-working ponies, who make the seasons change and manage the weather to fit their needs, so everypony has enough food and water, and every animal is also attended to assure that any of them are caught in the changes of seasons.

But what about the planet itself? What about Mother Nature?
This is the question that Gaia asks when she arrives to this foreign world. After so much work her son persuaded her to take a long vacation in Equestria, saying that she needed one and assuring her that he would be in charge now, and she must take a break. But what can a several billion-year old alicorn possibly do to pass her time in this land?

(SimEarth/MLP Crossover)
(Timelife of Gaia's life 'till the start of the story)

A machine made for war awakes in a new world. Stuck in surroundings which puzzle it; can it, or will it be able to become something more than what it is?

Crossover with Keith Laumers Bolo-verse
Other tags include : Slice of Life, Possible Romance believe it or not! And a bit of humor.
Please beware of any spoilers in comments as well

This story is a sequel to Ponies, Pirates and Peculiar Psychopaths

Chrysalis has been driven out of Canterlot, her invasion defeated. However, an old friend from her time before becoming queen is more than happy to help her succeed with her plans.

Will these two achieve their goals, conquering pony-kind and ruling over them with iron fist and hoof? Or will they be stopped in time, preserving the peace that Equestrian has known for as long as can be remembered? There is more than just dreams of world domination at work, though, this is personal for Chrysalis and her rediscovered assistance.

Hopefully, the line that 'Evil never triumphs' will prove to be correct, or else a drastic change is going to descend upon not just Equestria, but the entire world.

Thanks to Avatar of Madness for the coverart.