The first story in The Journey of Graves.

Ponyville is getting ready for the arrival of Princess Celestia's marshals, elite of royal guard and travelling heroes of the people. But in all the hustle and bustle of party preparations, a lone traveler slips into town, a young man with business concerning Twilight Sparkle. What that business is remains to be seen, but you can be sure Ponyville won't make it easy for him.
After all, where would be the fun in that?

Princess Twilight Sparkle discovers a centuries-old mystery hidden in the Royal Archives. Her investigation leads through layer after layer of deception and misdirection, setting her hooves on a path that seems to be leading to a mysterious secret. Along the way, she learns that some friendships can be very, very strange.

Book 1 of the Alicorn Adventure series.

AUDIOBOOK by VisualPony
Featured at the Royal Canterlot Library
TV Tropes Page (Courtesy of Sandtalon)
Goodreads Page (Courtesy of Facedeer)
Equestria Daily Page

WARNING: Major spoilers in the comments. Takes place several months after the end of season four. (Not a Da Vinci Code crossover, BTW!)

Do you see a dark tag? No, you don't. Not dark. Well, okay, there are a couple of dark-ish bits, but that's all. Not enough to warrant a tag. Speaking of tags, there really ought to be "Badass Twilight" and "Friendshipping" ones.

Sequels and side-stories (and more) can be found here Offprint and AO3, and a hardbound two-volume set of all that can be ordered from The Ministry of Image.

My editor for the first edition of this story was Gogito, and I can't thank him enough for all the hard work he did. My editor for the revised version was PresentPerfect, and he did a terrific job of getting the story into excellent shape.

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)

In 2185, during his campaign against the Collectors, Commander Shepard discovered a previously unknown species whose origins predated any other race in the modern galaxy. Following a daring rescue from their ancient sanctuary, the Equestrian Herd was brought back into the galaxy where, for the first time in eons, they must walk their own path.

Knowing full well the terrible threat that lingers on the edge of the galaxy, the leader of this newly freed race fights to secure her people’s future while attempting to prepare for the storm on the horizon.

This is her story.
------------------------------------

The long awaited Sequel to Mass Effect 2: The Equestrian Equation This is a reader directed story. Your choices will shape events.
If you favorite, also like! It's one little button click that makes all the difference.

Also, this series has its own TVTropes page now! (Special thanks to user CrowMagnon for setting it up).

Note: contains violence and blood

In the future, Rainbow Dash and Octavia become 'Bounty Hunters', hunting for the heads of criminals they are hired to kill. They never failed a contract- that is, until they spotted Twilight Sparkle on their list. Now Rainbow is torn between her own survival and her childhood friend's, but when time comes- loyalty prevails. As they battle against an organisation larger than they could ever imagine, the first signs of war begin to show when intel suggests that someone is attempting to assassinate royalty.

A story that includes blades, guns, gangster hats, blood, and loyalty.

[Anniversary Update:
-New scene in Chapter 8
-Edited and formatted
-A few things about the fic after each chapter
-New cover image]