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 Eljunbyro

A broken party of friends struggles to reunite.

Rainbow Dash continues to fly east.

This story is a sequel to My Little Heartbreak: Meanwhile, Back at the Farm

It has been settled. This month, Twilight and CO agree that for Heartbreak to live in Equestria, she needs an actual place to live in. A real home. With money tight, and Heartbreak not having much of anything of her own, how are they going to get her this dream home?
The answer will drag both Heartbreak and Rarity kicking and nearly screaming through a series of seemingly unfortunate events involving travel, discovery, and later on: The Cutie Mark Crusaders!
But there are dark secrets still being harbored within both Heartbreak and her new home. Will Rarity, a pony who prides herself on her looks, charms and grace be able to teach a pony who doesn't care about any of those things anything about generosity? Hopefully. And hopefully before one of them strangles the other.

It is the year 2038, and the Earth is slowly being consumed by a space-borne monstrosity dubbed the Black Tide, which is using nanotechnology to remake the planet into something hideously alien.

Erin Olsen works for Project Harmonics, humanity's last-ditch effort to find a new world before the Tide can wipe them out. But when that world is found, and it turns out to be occupied, Erin will need to find the courage to face the unknown in order to save the inhabitants of both worlds.

(Many thanks to Easteu for the fantastic cover image for this story!)

Now with its own TV Tropes page

There is now a follow-up to this story: Sunflower - Side Projects
Sequel: Project Sunflower: Harmony

Twilight Sparkle wakes up one morning to a harsh dose of unreality. She is stranded, without her friends, on an island which matches no known locale on Equestria. Surrounded and harried on all sides by the alien and the dangerous, she will find her mettle sorely tested, and find perhaps that the best friends you will ever have in your life are the ones you make when your back is to the wall...

Thanks to CedricBale and noobie56xx for tracking down the name of the artist so I could give them credit.

This story is a sequel to Austraeoh

Bellesmith is a pony who must perform experiments in order to keep herself and her beloved safe.

Rainbow Dash continues to fly east.