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

Twilight isn't having a very good day. An experimental spell blew up in her face, an army of changelings is attacking Canterlot, and she just died. Yet somehow, it looks like it's going to keep going downhill from here.

Given the chance to correct what's gone wrong, Twilight swears she's going to fix all this even if it kills her. Which it will. Frequently.

Cover art by Pixel Prism
Spanish Translation
Series TV Tropes page

Twinkie Pie. Appledash. Rareshy. You know these pairings and may have favorites of your own. But what if every member of the Mane Six were paired with every other member in the same fanfic?! That's what the Combinatorics Project is--an epic treasury of fifteen ships spread across five parallel universes increasingly full of plot and whimsy. Can you guess which couple is which?
* The angster and her secret admirer
* The burlesque showmares
* The celebrity marriage
* The commune farmers
* The curse victim and caretaker
* The dessert caterers
* The hopeless homebodies
* The industrial mavens
* The mad scientists
* The masquerade hosts
* The model train overlords
* The multiversal adventurers
* The orchard grafters
* The rivals in love
* The weather aficionados
Plus: Twilight blows up like a balloon and goes out to 'have a spicy time'! Applejack and Rainbow Dash are competitive about everything! Rarity dresses like a butterfly--and later in five outfits at once! Pinkiezilla crushes a miniature town and argues with Octavia about her instrument! Fluttershy dances with an angel and keeps a weather diary! Derpy tells a six-word joke! Not everypony ends up happy, but most do! A little suspense is a good thing. Bitter sorrow! Transcendent joy! Probability cupcakes are cupcakes that cupcakes!
Note: This story was written during Season Two, so a few small things are out of date.

Twilight Sparkle and her fellow Elements of Harmony have faced down supernatural foes of the highest order, but sometimes the deadliest danger can come from places one would least expect. As Twilight is forced to bear a devastating secret, her efforts to keep the Elements together may well tear them all apart.
The plotline of the thrilling Pony Psychology Series continues with an exploration of deception, despair and Discord.
This series takes place between Season Two and Season Three.
Secrets and Lies shares the Pony Psychology Series TVTropes page.

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.