This story is a sequel to The Legionnaire

The settling of dust is so often perturbed by the second motions of its disturbance.

This is a series of one-shot tales about the aftermath of the events that took place in The Legionnaire.

Freed from her entombment, Cozy Glow finds herself a student once more. At Twilight's behest, she embarks upon a new programme of friendship study, under the watchful (and suspicious) gaze of Twilight's protégé, Luster Dawn.

As she embarks upon her studies, Cozy Glow finds herself reconsidering everything she once took for granted, and Luster finds herself wondering what circumstances could have led the filly down the path of destruction she'd chosen. Yet Equestria seems far from ready to accept the filly who almost brought the empire to it's knees - Legion of Doom or not.

Cozy Glow has long abandoned the lands of Equestria, carrying her burdens with her. Too many mistakes to count, she deserved to be alone. All she wanted was to get rid of her regrets inside her head. Even being an alicorn merely made the pain only a little more tolerable.

Spike is the last one left after the rest of Equestria's defenders are defeated and imprisoned. He's now on a mission to find help outside his homeland, where he finds a powerful alicorn filly.

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

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

It has been two years since the events of Yu-Gi-Oh! 5D's. The Fortune program had been successfully installed into the Momentum Network, ensuring that it would never go out of control again and it seems that all is at last right with the world.

But when Yusei hears the voices of his Equestrian friends crying out through an anomaly in Satellite, Yusei revs up his D-Wheel once more! An old foe has returned to finish his mission once and for all, and it's up to Yusei to stop him! Can Yusei find and stop the sinister Paradox before his time-jumping destroys Equestria and his future?

This wasn't supposed to happen, but I said that I could come up with a sequel if I wanted to and my brain mistook that for an order. This story was born as a result. So hang on tight, my bronies! This is gonna be one hay of a ride!

DISCLAIMER: My Little Pony! Friendship is Magic, all Yu-Gi-Oh! characters, and the Yu-Gi-Oh! Trading Card Game are copyright their respective owners. All original story elements, including original cards, their names, and their effects, are mine and may not be reproduced without my consent.

Bioshock meets MLP in this psychological thriller, where Celestia's new faithful student, Siren Song, must discover the truth behind the city beneath the waves.

Beautiful, gifted, and faithful student of the Princess of the Sun, Siren Song has very nearly everything a pony could want. Sometimes though, in the twilight hours, Siren can see the sadness in her mentor's eyes. Once, ponies whisper, the Princess had another student named Twilight Sparkle, but she left Equestria, never to return. The pony who has a perfect life just needs one more thing—to convince Twilight Sparkle to come home so the Princess will smile again. But when Siren arrives in pursuit of Twilight, she soon finds herself trapped in a city of horrors, with only its monstrous denizens for help.

Now with a TV Tropes page!

Daring Do cannot believe her luck when she is asked to help explore the most ancient tomb known to ponykind. But terrible danger awaits her, for beneath the earth rests something beyond equine understanding.

Warning: comments contain ending spoilers.

TVTropes page.
Alternate ending by Duplex Fields.
Archived in the Pony Fiction Vault.
Reviews:
One Man's Pony Ramblings
Louder Yay
PresentPerfect
The Royal Guard
Cleverpun's Critique Corner
The Goodfic Bin

Ponyville is shaken to its core when a body is discovered in the Everfree Forest. As the townsponies grieve, the mysterious Special Agent Bentgrass from Their Majesties' Royal Investigative Service arrives at the Books and Branches library and drags Twilight into a world she's only read about: lies, corruption, suspicion, and murder.

Faced with an indifferent police force, and Agent Bentgrass's infuriating methods, Twilight must put the pieces together and catch the killer. But as blood continues to spill and questions pile up, one thing is terrifyingly clear: in the dark of the Everfree, much more is at play than mere murder.

Isolated from her friends and taken prisoner in the middle of a war, Twilight must deal with the very real dangers of being percieved as an enemy as well as the nightmares of her arrival on 'Earth'. Can she overcome her own fears and the fears of her captors? Will the wayward unicorn's assistance be a boon or a curse to the 'humans?' Most importantly, will she ever find her way home?

"In short, it's a story of friendship and plasma rifles, with the emphasis on the friendship. The characters are well written, the XCOM setting is fleshed out very well, and the story is compelling. If you love XCOM, you'll love the story, but even if you've never heard of it, it's more than worth giving the first 3 chapters a read.

There's excellent action later on, but the real strength lies in the collision between the friendly and naive world of Twilight Sparkle and the desperate world of humans fighting a losing war for survival and willing to do anything to turn the tide."

--Arzoo

(XCOM/FiM crossover)
(Cover art commissioned by a friend and created by the magnificent FoxInShadow!)
(Original cover art by the amazing Carnelian can be viewed here!)
(Gore tag for blood and some violence)
(Many thanks to the studius OminousTen, Arzoo, xXFluttershyForeverXx and finally Setokaiva for giving my rambles a once-over)
(Now with it's own TV Tropes page! Get to tropin' folks!)