This story is a sequel to Dusk and Dawn

The Dawn Militia and Nightmare Moon's armies continue to wage war across Equestria under the eternal night. The six bearers of the Elements of Harmony–Fluttershy, Rainbow Dash, Applejack, Rarity, Pinkie Pie, and Trixie–have been blessed with extraordinary powers, with which they lead the Dawn against the tyrant and her reluctant lieutenant, Eclipse.

But it's hardly easy. After all, what place does harmony have on the battlefield?

====Originally Written June 2011=====EQD Link====
There is a shadow to all of existence, a place that all worlds are shielded from by a thin veil. A Dark Place, where a single presence plots and struggles to consume all creation with its darkness. The author Alan Wake is one who has defeated this Dark Presence, but to save his wife and his world Alan had to remain trapped in the darkness.

Now, through his struggles to return to his wife, Alan has unintentionally released the Darkness and an old villain upon Equestria. To fix the mistake, Alan starts a new story with Twilight Sparkle as the protagonist. Can the unicorn find the strength to face the darkness, or is all of Equestria doomed to be the victim in the dreadful horror story?

Note: Story assumes no preceding knowledge of the game Alan Wake. Written for any MLP:FiM fan to enjoy.

After visiting the past in It's About Time, Twilight spends some quality time with Princess Celestia before returning to Ponyville. She then falls into a coma and wakes up where no living pony would ever wish to be, and things only get more complicated when Celestia gets an unexpected visit from herself. Featuring Twilight, Celestia, Luna, The Underworld, and some other alicorn etc.

Twilight is invited to Canterlot to compete with some of the greatest magicians in the world for the Moonstone Cup, a prestigious award for the most powerful and skillful magicians, unicorn and otherwise. Can she win? What sort of competition will she face?

Awesome cover image was taken from NoOneBahtim

Twilight and her friends are approached by Princess Luna who presents them with a set of questions that trigger a long and perilous journey.

Did you ever stop to wonder what became of Trixie, Gilda and Blueblood after your encounters? What did these episodes truly mean to you? What role will they yet play in the lives of the Elements of Harmony?

Last, are these questions as relevant as the journey towards the answers? Who will benefit from seeking these answers - you, them, or I?

Black Star is a rare talent in the field of black magic. After many years of study she is on the verge of something amazing, tantalizing and by many thought to be impossible. The summoning of a spirit from another realm. If she succeeds, this new spirit will be the first to grace the world since the six in the beginning of time. From the shadows her benefactor is looking on with interest. But is this really the ultimate goal of the research she's been put in charge of? Come with me into the world of Spectrum, and follow the lives and adventures from several walks of life. There are influential ponies from the military, the spirit from another realm, and even a little family from North Bay, all trying to survive what the world throws at them.

Before we begin, I have to warn sensitive readers that the story centers on a sensitive subject; the exploitation of others in some form or another. The gore in the story is mostly light, but the dark and tragedy tags are not on this story by accident. There are some pretty grim moments, but there will be a light at the end of the tunnel. I think... maybe...

PS: This is a story in the same universe as True Colors. But it is intended as a standalone story... for now… okay it will intertwine with True Colors but can still be read on its own.
PS nr2: Twilight and Nightmare Moon are background ponies in the story, but the while be popping up every now and again.

(Original image from deviantart: Fleur-de-Lisby by =Raidiance)

Twilight wakes up with a serious head-ache caused by her horn spontaneously growing due to a sudden increase in her magical power. Nopony seems to have an answer for it, but it has attracted the attention of an unusually powerful militant foreign nation intent on her capture and execution. When a string of events lands Twilight before Celestia's father himself he tasks her and her newfound magic with tying up some loose ends he'd left behind long ago, ultimately connecting with this foreign nation's goals. With their powerful enemy baring down on Equestria, intent on taking it in a stranglehold, Twilight and her friends have little other choice than to travel the world and hunt for the rest of Celestia's family and end several thousands of years worth of feuding to prevent the war coming to Equestria before they themselves are caught.

Image Picture by Lostzilla of DeviantArt.
(find him yourselves)

Ech is a whiny bitch, but he helped edit a little I guess. (you too bats)

Luna discovers something hidden from Celestia for twenty years, now, with emotions running high, she enlists the help of the Mane 6... but what seemed to be a single mystery, soon reveals a darker and much more complicated plot that will soon decide the fate of Equestria.

Check out the Empty Room TV Tropes Page (Warning: Spoilers!)

Revised chapters edits and proofing (with many thanks) by: lammy, Trevor, Nick Nack, Fifth Alicorn

"It's so nice to see you again!" said the thing that was not Celestia. "Oh yes, I know who you are, Twilight Sparkle. I had a taste of your magic the first time we met. Mortals forget things so easily, I find. Allow me to refresh your memory: you tried to kill me. But you failed, Twilight Sparkle. You only mostly killed me. And I guess that makes you one very unlucky little pony."

After failing to stop Nightmare Moon in the ancient castle of the pony sisters, Twilight Sparkle is left with a scar that will permanently change the rest of her natural born life. As Twilight recovers from her ordeal, she finds that she is left with a difficult choice. Either live her life as a lie or sacrifice her innocence to protect the ones she loves. The path before her is set and she must now walk it alone. The sands of time continues ever onward, with everyone already trapped in its muddy depths. The sun will rise and the sun will fall. Waiting for its call, Death awaits for all.

Tags, rating, and characters can change.

Art created by:
http://cuteskitty.deviantart.com (top)
http://ventious.deviantart.com (bottom)

I just put the two together