Mystery. Love. Magic. Murder. Truth. These are all important elements in the murder mystery Fluttershy has written, and is now asking Twilight to read. But the novel stars 'Twilight Sparkle', and she wrestles with the metafictional dissonance involved in reading a novel about herself and her friends. Twilight must do her best to solve the mystery, reconcile her own feelings about this ordeal, and figure out just what Fluttershy is trying to say by writing all of this in the first place as the lines between fiction and reality begin to blur.

This is a thematic crossover with the visual novel 'Umineko No Naku Koro Ni.' No prior knowledge of Umineko should be necessary.
Cover art commission done by SynCalio

Twilight Sparkle is a princess. She has an important role as a leader of Equestria, which means she has to worry about what everypony thinks of her. So when she overhears a private conversation, she has to come to terms with how she feels about herself, love, and a certain somepony, all while weighing her public image against her personal desires.

A story set in the Who We Become series.

This story can be read with no prior knowledge of Who We Become stories.

Content warning: The non-con tag is for discussion about an event that happened before the story takes place, and is not depicted graphically. The sex tag is for consensual sex. This story contains depictions of homophobia, hate groups, and gay slurs.

Thanks to ArchAngelsWings and Eddie Grammar for editing
Cover art by Pasu-Chan

Twilight and Fluttershy go hiking and get all hot and bothered. Typical trashy shipping stuff goes down. All their friends start coming out as well. Also Celestia nearly dies.

There we go.
I hope that appeases the manchildren that didn't like the previous story description.
Feel free to complain in the comments about how a romance story about horses from a show for children has somehow offended your conservative sensibilities.

I'm going to make a delicious sandwich out of black forest ham.

With Twilight Sparkle still adjusting to life as a princess, Rarity becomes convinced she can help her friend by finding her a special somepony. And when that somepony turns out to be Fluttershy, awkward dates and adorable moments are sure to follow!

Cover art by mocha-creme (Thanks to OminousBrony for the suggestion!).

For a different take on the same characters, be sure to check out my RariTwiShy story, Our Lady's Courtship.

When Spike falls ill with a life-threatening disease, Twilight must race against time to find the cure. After much research, she discovers a little-known potion that can save him, but all of the ingredients can only be found in the place that she fears the most: The Everfree Forest.

Even though it’s the middle of the night, the clock is ticking and Twilight is determined to save her oldest friend. Not wanting to go in alone, she enlists the help of her friend, Fluttershy, both for her reassuring presence and her impressive knowledge of the forest. The two of them embark on a dangerous adventure, where they will find challenges both in the environment and in each other.

Edited by The Abyss

Fluttershy has a crush on somepony, and her best friend wants to help her with her love life. Will she make it or will she be too shy to confess? Warning: contains femslash. If you don't like it, don't read it! There will be some AppleDash in future chapters.

This fic isn't part of She Knows How to Treat a Lady and its sequels.

Original pic belongs to IraeCoal, here's her dA, make sure to check her out, you won't regret it!

Sequel its now up! A Bell's Sonata Magic of Love Part 2

Twilight goes down with a sickness known as Hornflu a week before Winter Wrap Up, and is left in the care of Fluttershy. There, she is quarantined until the diesease dies off. However, both are harboring secret feelings towards the other that just refuse to be known. What will come of this and, worse, their unexpected fate?
Image is by KP-ShadowSquirrel from Da. Used with his permission.

This story is a sequel to A Bell's Sonata Magic of Love Part 2

After two years of marriage, Twilight and Fluttershy have a daughter to take care of. Learn how the little filly came into their lives and more in this final installment of Magic of Love!
Prequels: Magic of Love A Bell's Sonata: Magic of Love Part 2

Cover made by Athene112

Twilight has been thrust into a prominent role in equestrian society; a role for which she is woefully unprepared. With her coronation only three weeks away, she must prepare herself to meet the expectations of a nation. Thankfully, her friends are on hoof to provide her with their unwavering support on the run up to this momentous occasion.

However is their help what Twilight really needs? She wants to be a good princess, but is she willing to reinvent her entire personality to do so? Can anypony truly understand what she's going through?

Twilight had been warned dark magic was dangerous. She thought she could handle it. Unfortunately dabbling in dark magic has left Twilight with a deadly disease that there does not seem to be a cure for. Will she succumb to the darkness, or will friendship and love be enough to make the remainder of her time happy?