This story is a sequel to Fortresshy: The Nine Fathers

Fluttershy has returned to Equestria after being temporally displaced to another world, where she was raised by a loving but insane family. She didn't return alone, though. Her new family came back with her, now working for Princess Luna, their new Fortress being built near to Ponyville. All involved would need time to adjust.

Unfortunately, time waits for no one, pony or human. Still, the former RED Team - now Team RED MOON - is used to handling craziness. After all, they live under the same roof.

-----------
Part of the PWNY-verse.

Edit: New fan art by G_Haze, who also did the cover art!

A former pink pony finds herself in a new, hostile world and a new friend who's perhaps even more hostile. A small, angry man finds himself with a new friend he didn't want. Can they make it through this new misadventure together, or is it the universe that needs to watch out for them?

Cover art used with permission from Technaro.

A Guide to the past millennium and a half, including the final years of the Equestrian Republic, the Reign of Discord, the War of the Bloodied Crystals, the Lunar Rebellion, the Decade of Accelerating Change, and everything in between.
Compiled by Princess Twilight Sparkle.

We have a tvtropes page! It desperately needs some love: clicky

In response to threats of a griffon attack on Equestria, Twilight responds with a letter detailing just why such actions would prove unfavorable for them.

Supplemental slice of life chapters to The Wheel and The Butterfly

A misanthropic man finds himself sharing an apartment with a bubbly, hyperactive girl. A pink pony turned human is doing her best to adjust to a new world. Together they will get through sharing living space without killing each other... probably.

Cover art created for this story by the incredibly tallented Technaro.

Previously, in Dragon's Maw...

A place for collecting short stories that occur on the fringes of Fallout is Dragons, a Fallout: Equestria tabletop campaign.

Third main installment in the Tutelary Spirit universe. Recommended reading order: Loyalty, Honesty, Generosity, Kindness, Laughter, and Friendship.

In an urban metropolis, many ages after the original adventures of the Elements of Harmony, a young unicorn finds the Element of Generosity. And as the living embodiment of her Element, Generosity, like the rest of her friends, is always willing to guide and teach a pony of Equestria.

Cover image belongs to Soul-Soar.

Second main installment in the Tutelary Spirit universe. Recommended reading order: Loyalty, Honesty, Generosity, Kindness, Laughter, and Friendship.

Many ages after the original adventures of the Elements of Harmony, a hybrid mare crosses the countryside, searching for the Element of Honesty. And just like the rest of her friends, Honesty is no longer just a simple bearer of her Element anymore.

She is her Element.

Cover image belongs to turnipBerry.

Edit: installments are now multi-chapter. Explanation here.
First main installment in the Tutelary Spirit universe. Recommended reading order: Loyalty, Honesty, Generosity, Kindness, Laughter, and Friendship.

Many ages after the original adventures of the Elements of Harmony, a young stallion soars high into the clouds, searching for the Element of Loyalty.

Her original life lived and gone so long ago, Loyalty, like the rest of her friends, has changed and grown over her many lifetimes to guide the ponies of Equestria.

Because even after so long, the Elements of Harmony will always share their lessons of friendship.

Cover image belongs to Nyarmarr.

Red Team had been given an assignment. It wasn't the usual sort of assignment. They were assigned to defend their base 'until further notice'...and then never received notice. All announcements sounded pre-recorded, and enemy assaults were few and far between. The enforced inactivity was slowly fraying the bonds of the team...

...until something unexpected arrived. A tiny creature appears one day in their fortress, in need of compassion and care. Somehow, she finds that in this group of strange individuals, as she becomes their baby.

-------------------
Crossover with Team Fortress 2.
Part of the PWNY-verse.

Edit: Since I get these comments a lot, I will say here, I've never played the game and don't intend to include much in the way of game mechanics, so please don't suggest such things.

Edit 2: FAN ART! for chapter 9 by G_Haze. Makes me so happy.
Edit 3: More fan art from G_Haze, This guy's amazing!
Edit 4: New fan art! by The Pyromanecer. Thanks so much!
Edit 5: More fan art by shiningkord98.
Edit 6: New Fan Art by The Pyromancer
Edit 6: More awesome fan art from G_Haze! So awesome!
Edit 7: New fan art by Pioneering Author