Long ago in a distant land, I, Nightmare Moon, the shape shifting mistress of darkness unleashed a never-ending night! But, a foalish pony warrior, wielding a magic stone stepped forth to oppose me! Before the final blow was struck, I tore open a portal in time and flung her into the future, where my darkness is law! Now the foal seeks to return to the past, and undo the future that is Nightmare Moon! (FiM/Samurai Jack fusion)

One by one, Twilight and her friends must come to terms with the consequences of being the Elements of Harmony.

These stories take place in the intervening time between Season One and Season Two,
with the exception of Ditzy Doo: Muffins, which takes place early in Season One.

The series continues in the sequel, Secrets and Lies.

Pony Psychology has a TV Tropes Page.

Six fates, tied into one. A single moment that transformed the world, and set six young fillies on a course that was to intertwine them forever. How strange the ways of friendship and magic, and how mysterious the handmaidens of fate that work behind the scenes to make miracles happen...

Pinkie is given a special gift that gives her a window into a fandom they never knew existed. But when she shares this with her friends, things don't go exactly according to plan. On top of that, a special mission from the mayor? Timing couldn't be worse

Written for the enjoyment of the fan community on /co/ during the three week episode drought after Call of Cutie, this comedy is, nevertheless, very enjoyable to any fan. Modeled take place like an unlikely episode and remain in character, keep in mind that due to the nature of /co/, there is an adult reference warning.

When Twilight Sparkle and her friends awaken in the Everfree Forest following a spell cast by Twilight, they attempt to find their way home. However, what they stumble on to is more than they could have expected, or imagined, in their wildest Nightmares.

Celestia makes sure to surround herself with the most competent staff
in all of Equestria, but when they go too far in her service, she takes
things into her own hooves.

- Act I - Act II (You are here) - Act III

Twilight Sparkle has been forced upon a revelation. The life she thought she had is not real. Her memories are deceptive.

As Twilight tries to establish a hold on her new life, she realizes that her actions have consequences, even if she doesn't remember those actions. An embittered stallion eager for revenge against Twilight tells his story, and Twilight realizes just how precarious her situation is.

Meanwhile, and a world apart, a group of six ponies led by another Twilight Sparkle desperately search for a way to rescue their friend before her identity gets her killed. Rainbow Dash uncovers clues about her counterpart's past in the form of an old friend.

The appearance of an enigmatic mare with unknown motives threatens to complicate the rescue plan and warns that the interaction between the two worlds is more than anypony initially thought, for plans have already been set into motion.

Act I can be found here: http://fimfiction.net/story/92
Act III can be found here: http://fimfiction.net/story/5197

Inception inspired Pony time!

Princess Celestia has been trapped within her dreams. Princess Luna requires the help of Twilight Sparkle to rescue her sister from whoever has trapped her inside her mind, but as they go deeper into dream layers the more they risk losing their memories and even their own identities.

A thousand years is quite the generation gap, so Princess Luna decides she has to get with the times. However, this isn't quite as easy as she thinks it will be...

Celestia and Luna were born as unassuming foals in troubled times. But already marked for greatness, the simple earth ponies stand to face a world set against them, full of danger, fear, and sadness. A world they will change forever.

A sweeping epic taking place before Equestria was made, where Celestia and Luna must rise from normal foals to become the Princesses we know them as, beset from all sides by monsters, other ponies, and even the forces that govern nature. Their tale is as tragic as it is triumphant.

Currently on hiatus. For more info, go here.

(Cover and internal art by Madmax)
(Editing credit predominantly Lightside Luc)