https://www.fimfiction.net/story/418440/those-forty-years (The sequel is out! Check it out here. Check out my latest blog for why it's on my co-author's profile instead of this one.)

A legendary magical discovery leads the protagonist Twilight Sparkle through a chain of events that not only explain Celestia and Luna's history, but a history about herself that even she could not have imagined.
Co-Author profile link.

WE HAVE COVER ART! 8/3/2016 Check the source for the artist. (permission was given)

What happens when the entirety of Equestria, if not the fate of the whole world, relies on the shoulders of just 6 heroes and their companions? Did anyone dare to question what would happen to the future if those heroes can no longer bear the burden one day, and those believed vanquished rise again?

Twilight Sparkle, Starlight Glimmer & Spike have witnessed the outcome of such dependency; a future without the bearers of the elements. Chaos, darkness, conflict, fear, anguish, sorrow and ruin. And their only response to that was acceptance, rehabilitating Starlight Glimmer to be part of their ranks so perhaps she could make a crucial difference.

But there are many more events aside from time manipulation that can cause such dark times. The heroes triumphed over many fiends and challenges that brought everybody to the brink of doom. Even those they reformed narrowly managed to save their land from rule through fear and intimidation by the former changeling queen's hooves.

Ultimately, it does not change that time could be running out for them and this world at any minute. There might be no future in anything they believe to have accomplished while everyone else spectated powerlessly. False hope sown by narrow minds only reaps exasperation after all. But all inhabitants of this world deserve something else, something nobody could never achieve on their own.

A future of lasting harmony.

twilight goes back in time to save Equestria. By doing so, she accidentaly teleports the corpses of the mane six with her. They went back to the time where they met Chrysalis, because that's where it all went downhill. But her spell didn't only bring her back in time, it also replaced two creatures, switching from roles. If Chrysalis was now a good guy, who was the bad guy?

sequel to How Starlight Glimmer Actually Reformed

Starlight Glimmer is now Twilight's daughter!
But how does this effect the elements of harmony and Equestria?
First thing's first, Twilight will have to tell her parents about their sudden granddaughter. Then they're going to have to talk to both princesses about the new legal princess who happens to be an ex-villain. Hopefully her brother and sister in law will understand. Then there's Twilight's friends, the town Starlight controlled, and many problems only the elements of harmony can handle.

Sometimes she wishes she could go back to the days where she raised a young filly, Starlight...

Based off of this Comic from doubleWbrothers
The beginning of the Daughter Starlight Timeline

Starlight Glimmer caused some troubling problems with Twilight and her friends. What past caused this pony to go down such a path? How did Twilight fix such a horrible past to make this pony better?

Check out the sequel

This story takes place during the Season Five finale, "The Cutie Re-Mark". As such, there are spoilers ahead.

Starlight Glimmer's plan is working. All she has to do is upset Rainbow Dash's rainboom-creating race in the past, and Twilight Sparkle's connection with her friends will be severed. And she's done it. Repeatedly. Sure, Twilight can go back in time to try and stop her, but Starlight will always be brought back as well. No matter what Twilight tries, no matter how many times she returns, she can't stop Starlight. They're evenly-matched, and it's much easier to disrupt events than it is to preserve them.

That means Starlight wins, right?

While trying to fix Starlight's meddling with time, Twilight winds up face-to-face with herself. As she prepares to leave, her other self tries to persuade her to stay and help save this version of Equestria. And her other self makes some pretty compelling arguments.

In a desperate attempt to thwart the plans of a power-hungry sorceror, Twilight Sparkle ends up displaced in time.

She finds herself in a world untouched by catastrophe of any kind. Everything turned out well in her absence, and her friends, who have missed her dearly for the last decade, are overjoyed to have her back.

Now she has a decision to make. Go to fight the foe she left behind, restoring time as it should have been, or stay and leave him be. All is well that ends well, after all. Right?

Much gratitude goes out to Sagebrush, who helped me untangle some of my messes!

As Twilight revisits Star Swirl's time spells she finds herself stuck in ancient Equestria.

Additional tags: Star Swirl

Twilight for a time. Twilight for a spell. Twilight for a time spell. A story about Twilight stuck in ancient Equestria.

When history is rewritten so that Equestria is doomed, it's not a hard choice to try to revert the timeline.

While battling Starlight Glimmer's interference with the timeline, Twilight is faced with a moral dilemma when she lands in a timeline which has weathered Equestria's trials almost as well as her own. How can the lives of those living there be balanced against her vanished world?