Canterlot... For centuries, Canterlot was the shining gem of Equestria, the pinnacle of pony society. Now, it’s a reminder, a bleak and monolithic warning to the world. 

Changed by the chemical and technological poisons that plague the mountain, an abomination of nature, I wander the greatest disaster Equestria has ever seen. 

... I will escape eventually, and when I do, I hope my friends still see me as Twilight Sparkle, and not the monster that hides among the ruins. 

(Spyro seriesXmlp) Spike's always been curious about his race, but then again what dragon wouldn't be when all they've ever known is ponies? So when a spell book arrives that may offer some answers to his questions, with a little help from Twilight of course, the young dragon is overjoyed to say the absolute least.

Though when things somehow end up going astronomically sideways, Ponyville finds itself playing host to three unexpected visitors; three scaly visitors by the names of Spyro, Cynder, and Ember to be exact, each bringing their own personal touch of chaos to the small town.

Soon awkward and unusual situations arise, tempers flare with destructive consequences, personal demons and ancient evils threaten to rear their long suppressed heads, and Spike learns that sometimes, if you wait long enough, love will find you.

Inspired by this piece of fan-art I found (not mine) featuring Spike and Ember, and the short comic 'Spyro's back'

Once upon a time over a thousand years ago, two sisters controlled the pony occupied kingdom of Equestria. To keep harmony throughout the land, the eldest was in charge of the daytime. Everyone morning, she would rise to the sky with the morning sun and shine her light amongst her subjects while her youngest sister rose with the evening moon. However, while the subjects praises and basked in the glory of the eldest sister, the younger sister’s night was left ignored and forgotten. Angered with jealously, she turned against her sister and attempted to dethrone her. Understanding that she needed an army, she looked to an interesting choice; the humans and anthros who had occupied Equestria. Because they lived far from the normal ponies and were considered social outcasts and were discriminated and shunned by the general populace, they agreed to fight for the youngest princess. There was a short, but great war between the two sisters and their armies and when the eldest won using the Elements of Harmony, she banished her sister to the moon and the humans and anthros were left to the mercy of the ponies. Their leaders tried to negotiate a peace, but the ponies would have none of it and they convinced the eldest that they should face the same punishment as the youngest princess. The eldest then exiled the humans and the anthros to a long forgotten continent on the other side of the word; the continent of Carthage. For a thousand years, the people of Carthage lived in complete misery and suffering as Carthage was ravaged by chaos and violence driven even further by a seemingly never ended succession of madman, kings, and tyrants. Little did the ponies know that banishing man and furry kind, they left humanity with a burning desire to vengeance and retribution. And little did they soon realize that Carthage would rise again….

This story is a sequel to Ascend

Congratulations, Twilight. With Celestia and Luna on their constitutionally mandated vacation, you're in charge of Equestria. The position of Regent is an honored and hallowed one. But maybe it's a bit early to congratulate you. After all, whether it's a nobility jealous of your ascension, or a military unhappy with Celestia's decisions; one thing's certain: your reign will be anything but peaceful.

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.

For a thousand years, the Code of Harmony has ruled Equestria, and the Code of Dissonance has sabotaged its works at every turn. Now the war for control over the land will come to a head, and one unicorn's decision may decide the fate of all.

For though she does not know it, Twilight Sparkle is the shining example of the Code of Harmony. Her teacher, Princess Celestia is Harmony's most powerful master and she knows her enemies are hatching a plan that threatens to cast down the Harmony of her throne and all she has sacrificed to create.

What she does not know is her foe seeks a new Apprentice to turn to his dark ways. A unicorn with seemingly limitless potential for magic, whose thirst for knowledge may yet lead her down a dark path, who is known to be such a faithful student of magic, eagerly seeking the truth no matter how forbidden it might be...

Sequel: Code of Harmony

Two hundred years have passed since the discovery of the purveyor and the events set in motion by Celestia's endeavor to save her own world. Now, the purveyor has returned from the void and their world will change, for the better... or for the worse.

This is the sequel to The Watcher, it is advised to read it before reading this.

A big thanks to Lord Destrustor for editing. Go check out his work, his stories are definitely worth your attention!

Twilight becomes alicorn of the stars. This is sort of a problem, because Luna kind of already was alicorn of the stars. Oops!

TV Tropes

This story is a sequel to Apotheosis

Celestia leaves Equestria in the hooves of Luna and Twilight.

While she searches among the gods to answer her questions, Luna and Twilight must struggle to fulfill their own duties to ponies and to Equestria.
Now with a Spanish translation by SPANIARD KIWI: https://www.deviantart.com/spaniard-kiwi/art/Apoteosis-3-3-857110357

This story is a sequel to Off The Edge Of The Map

When Twilight is sent with Luna on a diplomatic mission to Draconia, they quickly find themselves somewhere that doesn't appear on any map, and Luna is lost in more than one way...

Thanks to RBDash47 of Pony Fiction Archive for formatting it for submission.
Title image by Valcron

Tremendous thanks to Illya Leonov and Scribbler for the Audiobook version.
Now with a Spanssh translation by SPANIARD KIWI: https://www.deviantart.com/spaniard-kiwi/art/Apoteosis-2-3-857110089