After tiring of Twilight's hostile attitude, Discord decides to "help" the Elements of Harmony by bringing in an alternate version of each of them. These duplicates from various worlds aren't told anything about each other, which is good. The last thing Equestria needs is these monsters working together.

***Not too dark!***

Elements of Disharmony
Pinkie Pie from Cupcakes by Sergeant Sprinkles

Rainbow Dash from Rainbow Factory by AuroraDawn

Rarity from The Secret Life of Rarity by BronyWriter

Fluttershy from Pattycakes by Pegacorn Ondacob

Twilight Sparkle from Death Note: Equestria by Nonagon

Applejack from Bad Apples by... Bisque? It's hard to find an evil Applejack story.

This story is a sequel to A Stitch in Time

Having discovered the message left for her by Star Swirl the Bearded in the distant past, Twilight once again finds herself caught up in the middle of a struggle against forces far greater than herself. In order to even stand a chance she'll need to travel further and wider than she ever has, and forge some unlikely alliances with old enemies. All to bring down the powers that have manipulated and shaped her entire life, and retake control of her own future.

The conclusion of the Time Loop Trilogy, which began with Hard Reset
Available in Spanish thanks to dgs1993
Series TV Tropes page

The Great and Powerful Trixie receives a visit from her future self. Well, of course she does, being the most talented magician in all of Equestria... However, her future self dies before her eyes, telling Trixie that she has only four days left to live...

Trixie appears once more in Ponyville, but something is...off...about her. She isn't speaking in third person. She is convinced that she is supposed to be the Element of Magic, that Celestia is supposed to be the Tyrant Sun, that Luna is supposed to rule as Equestria's monarch - and that Twilight is supposed to be a wanted criminal. Has she gone insane? Or is something bigger beginning - with consequences that Trixie, Twilight, and two entire worlds, can only guess at?

The long-awaited Crisis on Two Equestrias begins at last!

While reading the stories of The Lunaverse can only enhance your reading experience, it is not necessary for this story! It is being written as completely, 100% stand-alone, with no prior knowledge necessary!

WANTED:

The newly crowned Princess Twilight Sparkle has set up a bold new initiative to discover new magic, and is sending out an open call to the unicorns of Equestria to apply for her research team. No experience in magical theory or research necessary. Enthusiasm and out-of-the-box thinking a must. The Equestrian government is not responsible for any physical, emotional, or magical trauma experienced during the course of the project or the application process.

Cover art by Page Turner

When the Cutie Mark Crusaders dig up an ancient magical artifact, they unleash a spell on the town that allows everypony to see a "lie meter" floating above each other's heads. While attempting to solve the mystery, Twilight Sparkle has to analyze the tenuous balance between friendship and honesty. She doesn't like what she finds.

Based on a story idea conceived by theworstwriter
Written and posted with his permission

Derpy Hooves is secretly a changeling.

Nopony particularly notices, or cares.

(New 9/15/19: Spanish translation by Spaniard Kiwi! Thank you!)

This story is a sequel to Hard Reset

After the events of Hard Reset Twilight's life and mental well being are slowly returning to normal. Her recovery is cut short, though, when a letter arrives informing her that the time loop spell she cast is causing severe damage to space and time itself. In over her head, Twilight tries to summon anypony who will know how to fix it. The pony she gets is the last one she ever thought she would meet... and nothing like she expected him to be.

Available in Spanish thanks to dgs1993
Series TV Tropes page

Trixie Lulamoon is causing trouble in Ponyville once again, in more ways than one. As somepony who would like to be Trixie's friend, and who doesn't want to push the problem onto somepony else, Twilight Sparkle agrees to help.

Two months have passed since the Alicorn Amulet incident. While struggling to get her magic act afloat again, Trixie finds herself filling in behind a bar in Manehattan, to work off a rented room upstairs. That night, just before closing time, she encounters journalist and adventure novelist Ember Roundup, who reveals that she has been trying to track her down for over a year, since the death of her best friend and writing partner - Trixie's cousin Gusty - as it seems Ember has a significant debt to repay...

Inspired by the Daring Do pages at TV Tropes - credit for the relevant OCs goes to Zarbi Nerada, Clato Lawa (AKA me) and Peteman.

Credit for the premise of Daring Do and the Amber of the Smooze goes to Jenny Nicholson and Griffin Lewis, for Friendship is Witchcraft

Credit for the premise of Daring Do and the Ruby of the Blank VIllage goes to Donitz, for Story of the Blanks.

Credit for the name Checker Monarch goes to Shadow Raikou and Godzillawolf, for Trixie's Gettin' Back On Her Hooves.