Twilight Sparkle wakes up one morning to a harsh dose of unreality. She is stranded, without her friends, on an island which matches no known locale on Equestria. Surrounded and harried on all sides by the alien and the dangerous, she will find her mettle sorely tested, and find perhaps that the best friends you will ever have in your life are the ones you make when your back is to the wall...

Thanks to CedricBale and noobie56xx for tracking down the name of the artist so I could give them credit.

Not so long ago, Equestria barely defeated two almost unstoppable creatures known as humans, which they called the Second and the First. Almost five years later, another one has shown up. The military takes up arms, the princesses are stricken with fear, and the Elements of Harmony assemble, ready for battle. But 'the Third' has no idea what's going on, and only wants to know how he came to be here, and how to get back home. Good questions indeed...But will he ever get his answers? Or will his predecessors' legacy catch up to him first?

“Side story/prequel to Human by DannyJ, but can be read on its own. Contains spoilers.”

This story is a sequel to The Wandering Physicist Adventures

Seven years after the wedding on Twilight Sparkle and James Wanderer, life in Ponyville is pretty normal.

Apple Bloom runs the library for Twilight Sparkle. Applejack and her son have a happy family life. Sweetie Belle attends music school in Canterlot, living with her sister in Rarity's new shop. Scootaloo works full-time for Rei, who is finally married to Inkie, while training to join Rainbow Dash as a Wonderbolt. Fluttershy and Sunshine raise two lovely foals of their own. Pinkie and the Cake twins work to make everypony in town happy. Trixie, Stormy and their daughter travel the world performing. Just normal life for everypony.

One day, The Master shows up in Ponyville to torment his old 'friend', The Wandering Physicist. Instead, he ends up harassing everypony TWP cares for as a distraction while he tries to conquer Equestria. Everypony will have to keep their wits about them to survive the threat of the deranged Time Lord and prevent him from destroying the land they love.

Sequel to The Wandering Physicist Adventures - Written in a manner so that all necessary backstory is covered within. No real need to read TWP, but it is appreciated.
Prequel to Starlight Chronicles

Character References: On tumblr - On Deviant Art - Warning: Contains spoilers and peanut products.

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

When a Necromancer is hurled into the place between places then escapes to another world at the cost of his life it is not the end. Being a Necromancer he returns to life with ease, but is skirting the edges of consciousness, and unable to truly wake as a mysterious figure uses magic to put him on the back of a horse to carry him away into the night.

To make matters worse the phylactery he used to save his own life recreated him as a member of the dominant race with... some errors. His injuries are still present and he's now in a much smaller body with his magic drained to nothingness.

So now he's horribly injured, held captive by an unknown force, in an unfamiliar body, in an unfamiliar world and completely exhausted. He's had worse days. He just can't think of any off the top of his head. So familiar territory then, nothing to worry about.

(Thank you again Tulip for the amazing piece of artwork.)

On Hiatus due to Life. Sorry.

This story is a sequel to Windfall

A brilliant mind discovers a problem in search of a solution, which leads to inspiration, which leads to invention, which leads to a technological/magical advance that will in time forever change Equestria.

Sequel to Windfall, set three years after the events in that story.

He was always considered an outcast, a black sheep. When his peers find his secret, that he likes to watch My Little Pony, they taunt and ridicule him for it. But, after a freak accident, he is taken away to the land of Equestria. Has he truly found his place? Oh, and he's an ork. That might be an important little detail. Warhammer 40k crossover.

FAQ for this story: FiM Fic version and GDoc version (constantly updated and edited)

The Wandering Physicist is a mysterious traveller who just arrived in Ponyville. After establishing himself in the video game shop, he begins his encounters with the denizens of Ponyville. This sets off many ongoing adventures with his new friends. With a constant stream of visitors from around Equestria, friendship, family, twists and turns and legions of nerds are on the horizon.

Setting: Approximately a year after the end of the series.

Character References: On tumblr - On Deviant Art - Warning: Contains spoilers and peanut products.

To new readers: These were written as an ongoing serial. The individual story does not necessarily carry chapter to chapter, but the continuing story and events carry over. Feel free to skip around the chapters without losing too much continuity. If you do not wish to start at the beginning, Crossroads is a good starting location as it lays down the groundwork most of what follow.

As this was a serial, there is a cast list at the top of each chapter allowing the you to read only those with characters you are interested in. The main characters listed are those that appear in the majority of the chapters.

Arcs:
TWP vs the World: The Game Arc - A Trixie Situation to Final Boss - Trixie is on the run from some nasty elements in her family. Ponyville is placed in gaming illusions to force TWP to turn Trixie over.
The Physicist's Wife Arc - The Physicist's Wife to Confessions - Fluttershy gets injured and thinks she is married to The Wandering Physicist. She spends a month living with her love, but what do her friends think of the new Mrs Wanderer?
Adventures in Neighpon - Turning Neighponese to Tomodachi Sketch - The Wandering Physicists takes his friends on a trip to Neighpon. A series of interconnected adventures take place leading to love, fortune, action and a giant alicorn plushie.

Prequel to The Master Game
Prequel to Starlight Chronicles

Jessica finds herself flung into a world she has little concept of. Everything is strange and new to her, but worst of all she cannot communicate with the native inhabitants. A world of monsters and sapient ponies, griffons and other assorted beasts is no place for a human girl.

How will Jessica cope? Without an understanding of their language how will she make her way in the world, will she even be able to ever communicate with them? Why was she even brought into the world and is there even a way for her to get home?

(Thanks to Tulip for the Cover image!)

(Also now apparently has a Tv Tropes page in the making. )

Now has a re-telling in progress focusing on the Equestrians' side of things, A Stranger Among the Voices

What if the villains were allowed to win without a fight? Would all of their plans bear them the fruits they so desired?
Probably not, especially when their royal adviser is Twilight Sparkle.

A collection of (continuous) One-shots in which our heroes don't have any epic fights with villains, and simply allow the power of logic to crush all of the hopes and wishes of the would-be rulers of Equestria.

Currently up: Nightmare Moon, Discord, Chrysalis, Sombra (bonus chapter - the fight is so not-epic it happens off screen).