Twilight gets a feeder to study birds.

She also bought a ton of seeds for it.

While she's frustrated at the fact her supply seems to be disappearing into thin air, she's about to realize that she has a much bigger problem on hoof.

Diamond Tiara has always enjoyed picking on the Cutie Mark Crusaders. But one day, she finds she's gone too far, and everything for her comes tumbling down. But help may come from the most unexpected of places...

Started before season four, and does not take season four canon into account.

This story is 100% Diamond Cutters Approved!
Note: If reading this inspires you to write your own Diamond Tiara fanfics with similar premises, send me a link, as I'd love to see them.

This story is a sequel to The Celestia Code

When the monsters created by the dark crystal engine escape their prison, it's up to Princess Twilight Sparkle to deal with them. She gets help and advice from Princess Luna, but things don't go as planned. In fact, when a pony who relies on logic and rationality tries to navigate the stormy seas of emotional entanglement while simultaneously saving Equestria from a horde of evil creatures intent on destroying everything they encounter, nothing goes as planned.
AUDIOBOOK by VisualPony
WARNING: Major spoilers in the comments.

Book 2 of the Alicorn Adventure series.

Goodreads Page
100% Approved by Twilight's Library!

The Badass Twilight tag applies more than ever, but please note the new tags.

This story is a fairly direct continuation of The Celestia Code. You might be able to follow it without having read The Celestia Code first, but it's better if you do.

The sequel is here: The Twilight Enigma

Most excellent pre-reading/editing done by the erudite AcademicPony and the dapper statoose!

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 Into The Depths

The horrors of the catacombs have turned to distant memories for Celestia, Twilight, and Luna. Discord’s change of heart and Twilight’s coronation have helped to ease and erase the mental scars from that harrowing night. The three princesses can even smile and laugh as Nightmare Night moves into full swing.

Yet, it should never be forgotten that those who have been touched by Tirek are forever within his grasp.

Octavia has hit rock bottom. After the Gala and being forced to play that song, she was cast out by high society. Now she must gather the shreds of her pride, only to have to swallow them to work under the only pony that seems willing to hire her. Now it's time for her to make a name for herself all over again, and she's determined to make it no matter what, even if she has to start over from Scratch.

Strange nightmares are plaguing the ponies of Equestria.

Somepony must help ponies to face their deepest fears, but unless Princess Luna is able to discover who—or what—is responsible, the nightmares may never end.

Scootaloo is ready to prove that she can be as fearless as her big sister, Rainbow Dash, even if it means never having a peaceful night's sleep again.

When Rarity has a chance meeting with Braeburn, a blossoming friendship is tested by the latter's sudden silence. Undeterred, Rarity chases the frontier pony to Appleloosa, determined to know what he is keeping from her and keep their connection alive.

She finds a new world clashing with everything she thought she valued, a town determined to push her generosity to the limit, and obligations tearing her in two directions at once. Amidst the dirt and sand, a search for friendship turns into something much more serious.

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Cover art by Ruirik

After returning from Hearth's Warming Eve in Canterlot Rarity cannot stop thinking about her purple unicorn friend in a new light. Great angst and shipping ensues.

One afternoon, when Twilight and Fluttershy are exploring antique stores, Fluttershy purchases a gem that claims to grant any wish she desires. Some may think she'd wish to have more animal friends, or to have better speaking skills. Instead, she wishes that she could fly like Rainbow Dash.
The next morning, Fluttershy wakes up. Except for one thing. She has no idea where she is, or why every pony expects her to go along with a lifestyle she never knew she had.
As a great unicorn once said, magic does what it likes. Sometimes, it changes all aspects of reality, and tweaks the future.