What are the chances your favorite pony was secretly a changeling all along?

Yeah, probably about one in one.

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

Blythe Hyacinth Pie, Blinks to her family, makes her annual pilgrimage to Tartarus to see her grandparents and hopes for their redemption.

When Spike asked Twilight to help him create The Noble Dragon Code, he hoped a lot of things would happen.

Getting worshipped as a god by legions of theologically-inclined dragons wasn't really one of them but, hey, whattcha gonna do? Them's the breaks, kiddo.

This story is a sequel to Justice

Worker's dreams have taken a turn for the worse. Feeling trapped, unable to talk about his experiences and unable to stop the near-nightly terrors, he wonders if he should reach out to the Princesses. It never occurs to him that these nightmares might be something more.
This is the final story of a trilogy. The first part is Order from Chaos, and the second is called Justice.

Darrilon has proudly served Princess Celestia for many years, and risen to the rank of Captain of the elite squad known as the Solarian Patrol. But every day is a new challenge when your superior officer (and divine ruler) has no respect for protocol or procedure.

Derpy Hooves is secretly a changeling.

Nopony particularly notices, or cares.

(New 9/15/19: Spanish translation by Spaniard Kiwi! Thank you!)

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

This story is a sequel to Order from Chaos

Worker has found happiness, health, and most importantly, home. Now he struggles to defend those who made his new life possible while he wrestles with his own demons.
A belated sequel to Order from Chaos.
Concluded in Hope.

A handful of pages recount a remarkable journey to Equestria by someone who sought only a little peace. The story continues in Justice, and concludes in Hope.