Spike is a dragon with mare troubles, and one of those mares just happens to be his mother. When he meets Lyra, who has troubles of her own, he hatches a plot that they think will be mutually beneficial.

Special thanks to Setokaiva for his proofing work.
Spanish translation by SPANIARD KIWI can be found here

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.

This story is a sequel to Twilight Sparkle And the Very Confusing Day

There were a few loose ends after Discord, who had turned into Eris, had gone into season and turned the entire world upside down in order to create enough chaos for favourable draconequus breeding conditions. Celestia had released the Flutterbeast upon Eris, restoring order and gender normality all over the globe.

Except not everypony and everybody changed back. Males who became mares and became pregnant, stayed mares, Eris' final parting gift of confusion and chaos in the world.

Both of the sexes are now so much more aware of each other's needs following the events of the Great Swap, and Eris' chaos had the unintentional side effect of creating a new level of harmony in the world, as suddenly everypony and everybody now had first hoof (or firsthand) experience in being the opposite sex.

Eris going into season also created the ideal conditions for the apocalypse.

Edit: Featured on Sunday, April 20th, 2014! Oh my gosh oh my gosh oh my gosh!

Now with 23% more sequel!

Twilight and her friends all get together for a sleepover, looking forward to some well deserved downtime. Discord arrives, standing outside in the rain, pleading for entrance and to come in out of the weather. Twilight Sparkle insists that this is a mares only sleepover, so Discord does the only thing he can do, doing the unthinkable to gain entry.

Once inside, Discord, now Eris, tries to bond with the mane six and learn the magic of friendship.

The mane six fail to take into account the magic of Discord.

Now featured on April 16th, 2014. Thank you all so very much!

The Cutie Mark Crusaders know that Babs Seed was bullied back in Manehatten, but how bad could things really have been? And how does Babs feel about returning to the city and the ponies who have hurt her the most?

(Note: to avoid confusion, the first few chapters of this story deal with past events that occurred before "One Bad Apple". I will add an Author's Note to the chapter that begins the "present" state of events and continues forward from there.)

Followed by Sweet Apple Anthology and Severed Roots.

Now with a TVTropes page! Thanks to vren55 for putting it up!

Rated Teen for some violence, language, and darker elements.

Luna and Philomena: a hate affair for the ages.

A thousand years ago, Celestia's pet harrier chases a broken Nightmare Moon through the Everfree Forest. A thousand years later, a much-diminished Princess Luna attempts to feed and take care of the elderly phoenix. In neither case does it go particularly well. Set during Season One, slightly before "A Bird in the Hoof."

Now with a Spanish translation by Spaniard Kiwi!

Diets can drive anypony off the deep end, and Sweetie Belle is about to find that one out the hard way. Meanwhile, Spike is apparently handsome. Because.

Wrote this one on a whim. I hope it tanks so I can get rid of it.

A regular human arrives in Equestria and to most it would be a dream come true. But this human knows pratically nothing about the ponies or their world. With no home to return to, he is forced to brave this new world. So he does what any human in his situation would do. He survives.

Rated teen for swearing, blood and how it gets kinda dark. Written after season two. Updated after season 4.

"Dear Princess Celestia, as your (former) most faithful student, I feel I have to warn you that this is probably a trap. Chrysalis cannot possibly be serious about this. Why would anyone, much less her, want to shoot a documentary on us?"

Chrysalis, queen of all the changeling hives and infinitely cunning architect of their plans to conquer Equestria, has a problem: She knows diddly-squat about ponies. But Chrysalis is cleverer than most—or all—changelings, and she's already devised a brilliant solution to this trifling issue: Make a movie about them.

Tenth place winner in Equestria Daily's Outside Insight contest.

Awake and alone, Applejack will find a way to survive.

And here's a TV Tropes page, if you're into that kind of thing.