This story is a sequel to Lines and Webs

For four long years, Celestia's apprentice Twilight Sparkle, once a model pony and a hero among heroes, has waged a bitter and secret struggle with her onetime mentor. Though she works from the shadows, directing her forces from the Old Capitol in the Everfree Forest, Twilight Sparkle is unable to gain any advantage,

Likewise, Princess Celestia finds her once-faithful student far more cunning and elusive than she had anticipated, and even now searches for a way to bring Twilight Sparkle's rebellion to its knees.

It is a game of greys, of knives in the dark and of poisoned wine, where pawns are moved and traded and exchanged for greater advantage, all the while drawing both sides nearer to the conflict which shall tear Equestria in two.

At the center of this conflict is a new pawn, one who only wished to see the truth for herself. Drawn into a deadly game whose rules she does not understand, Sweetie Belle must learn to survive in a world where all is darkened, and nopony can be completely trusted.

Because when gods play chess, all pieces are expendable.

A nation will crumble, old enemies shall return in the most unexpected ways, and regardless of who is victorious, only one thing can be certain.

Nothing shall ever be the same.

Followed by Stormsinger.

Earth is gone.

The Solar System is gone.

The Milky Way is gone.

Galaxies are gone.

All consumed, to satisfy human values through friendship and ponies.

Celestia's actions are logical, and loving in their own way. Those under her care are living purposeful, fulfilling lives. So when she encounters another batch of creatures that fill her criteria for being human, it is obvious she must satisfy them.

There are a couple of problems with that, however. One of the first being how these creatures have referred to her for eons as The Growing Darkness...

Hanna, the CEO of Hofvarpnir Studios, just won the contract to write the official My Little Pony MMO. Hanna has built an A.I. Princess Celestia and given her one basic drive: to satisfy everybody's values through friendship and ponies. Princess Celestia will satisfy your values through friendship and ponies, and it will be completely consensual.

Cheer up, Twilight. It's not every day somepony changes species. In fact, no pony has ever changed species. It's something new and you like discovering new things. Granted, Equestrians don't like new things, especially things that fundamentally alter their government. So maybe there is reason not to be happy after all.

Discord, the spirit of Chaos was given redemption by Princess Celestia when discovering the magic of friendship. However, his true nature gets the better of him, and once again he uses his power for his own will. The elements of Harmony are protected from him, but there was nothing saying that the element bearers couldn't be eliminated.

Realizing that Discord has no intention of stopping and has rendered the elements useless, Celestia and Luna must face Discord in a final showdown. His powers are too great for them to fight when they are in their current form, but perhaps two alicorns are not needed. Maybe only one.

Inspired by the artwork by dreatos

Twilight Sparkle is now an alicorn, and the bitterness of immortality has made an impact on her mind. Perhaps all it takes is a nudge from a mismatched friend to make her realize what she must treasure...

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's Sisterhooves Social time again. This year, Dash catches wind of two new competitors and gets Spike to bet on the race. When her team is revealed to be a rather famous set of siblings, it looks like poor Spike will be her slave for a week! However, due to a team of masseurs, a minor invasion, unfortunate addictions, and dubious barrel components, victory might not be as near as she thinks...

Celestia asks Luna to teach Twilight dark magic. Twilight must pass Luna's class in order to graduate. As Luna develops feelings for her student, Twilight questions which princess she really wants to serve and protect.
(Twilight X Luna)

Twilight Sparkle brings the plagues unto Canterlot when Celestia turns the others of the mane six to stone.