Twilight Sparkle's long journey had been aimless. Formless. A search for something she could not, or would not name. Her living, singing ship had plied the void for so long with no destination in sight.

But everything is different now. This is a mission of mercy.

Thank you to TheMaskedFerret for her help, and for being a friend when I needed one. And for ScarletWeather, who also read this and is also very good.
Cover Art from the animated "Echoes of the Past". Watch.

"I stood before the doors to Princess Celestia’s private chambers, just as I had so many times before, and waited. I’ve always been a nervous mare before our meetings, wondering if what I had done measured up to her expectations. But I had never before entered those rooms with the blood of another being on my hooves. I swallowed, dreading what I would discover behind those doors."

Twilight faces more than she bargained for when a resort island turns out very different from her expectations, and she must make a decision that will forever change how she sees herself.

A brave stallion goes on a quest to save the world by finding a lost princess in an enchanted forest. Things don't work out as he planned.

WARNING: Some spoilers in the comments. Also, a few mild spoilers for the Alicorn Adventure series, though it's not necessary to read those stories to understand this one.

Equestria Daily Page
Goodreads Page
Zabaware/AT&T Natural Voices "reading" by Modoc

As the details surrounding the Canterlot Invasion don't add up, Twilight investigates the suspicious disappearance of a guard during the attack.

This story is a sequel to It's a Dangerous Business, Going Out Your Door

EDIT: 6,000 unique views! Thank you so much to everyone who has read and enjoyed this story.

TVTropes Page

An ancient evil has awakened. No, really, it has. From the depths of time, a black, noxious threat has risen up after millennia of imprisonment. It washes like oil over Equestria, swallowing up towns and uncovering terrible secrets long buried. Twilight Sparkle, Applejack, Rainbow Dash, Pinkie Pie, Fluttershy and Rarity are prepared to combat this great darkness. However, to do so, they must uncover the truths about the Elements of Harmony, and the truths about the ancient forerunners of Equestrian culture. What they find will challenge their conceptions of their own places in history and ponydom's place in the world. The six Bearers of the Elements must draw upon their friendship and the strength of their hearts to stand firm against the darkness. If they fail, it will mean the end of everything.

To save her sister and her faithful student, Celestia herself must travel into the ancient tunnels beneath the ruined castle in the Everfree Forest. She, and the guards who accompany her, must face the dark, twisting corridors. Still, what was Luna and Twilight's purpose at the old castle? Why were they unable to return of their own accord?

And what watches Celestia from beyond the light's edge?

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.

When she was birthed with horn and wings she was thought to be a pegacorn, a rare and blessed blending of the tribes, whose long life and power brought wealth and stature.

Then the guards came, seeking the first alicorn born in over a thousand years.

An entry for The Most Dangerous Game contest
Now archived in Twilight's Library

One by one, Twilight and her friends must come to terms with the consequences of being the Elements of Harmony.

These stories take place in the intervening time between Season One and Season Two,
with the exception of Ditzy Doo: Muffins, which takes place early in Season One.

The series continues in the sequel, Secrets and Lies.

Pony Psychology has a TV Tropes Page.

After an unknown accident Twilight Sparkle and Rainbow Dash awake to find themselves sharing the same body! Now they must struggle to hold themselves together as their world is turned upside down. How long can two ponies exist in a single mind? It’s a race against time as they search for answers before it’s too late. When all is said and done, you’ll never look at Twilight Dash the same way again.