"It's so nice to see you again!" said the thing that was not Celestia. "Oh yes, I know who you are, Twilight Sparkle. I had a taste of your magic the first time we met. Mortals forget things so easily, I find. Allow me to refresh your memory: you tried to kill me. But you failed, Twilight Sparkle. You only mostly killed me. And I guess that makes you one very unlucky little pony."

It's been almost three months since Spike was cured of his werepony curse and things seem to be getting back to normal. Unbeknownst to him, however, Rarity has a surprise that will test his commitment to their relationship.

The story continues with Luna the Matchmaker

Don't know what the heck is going on? Then start to story right by going all the way back to the beginning with And Tootsie Flute Makes Three

Life is good for Lyra and Bonbon but something is missing. Bonbon wants more, she wants a foal and Lyra is faced with how to give the love of her life what she wants.

The story continues with Curse of the Werepony

An unfortunate turn of events finds Spike changed into an Earth pony. Rarity unintentionally crushed his heart and now she has to fight hard to win back his trust, his friendship, and maybe something more.

The story continues with Curse of the Werepony 2

Don't know what the heck is going on? Then start to story right by going all the way back to the beginning with And Tootsie Flute Makes Three

When dark creatures begin appearing in Equestria, Princess Celestia and Princess Luna summon the bearers of the Elements of Harmony to Canterlot. Before the six ponies can arrive, though, four strange ponies are expelled from a portal that appears in the throne room, and they explain that Equestria is not the only place at risk from these creatures. Thus begins an adventure that will reveal a greater destiny for Ponyville's librarian than she could have ever dreamed of.

Kingdom Hearts/My Little Pony: Friendship is Magic crossover. Pairings undisclosed.

Truth is the first casualty of war.

The world is in flux; new ideals, groups and technologies permeate every level of society in this age of discovery. The field of augmentation has allowed ponies to improve themselves in ways that were unthinkable a generation ago. Yet, for every benefit, there is an inverse. A griffon civil war rages on the borders, feeding the profits of mercenary companies. Rising populations have forced the rich and poor ever further apart. Harmony is dying.

Mortally wounded after a fatal attack on her laboratory, an earth pony researcher is augmented against her will and sent out into a chaotic world in search of answers. But as her quest unravels this chain of events, she discovers an ancient conspiracy that will shake Equestria to its very core.

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TVTropes Page

This story is a sequel to The Ambassador's Son

Lord Sapphire lays dead and Tacksworn is in ruins, but Chiphoof Irontail has come home to his adoptive father, Sharptooth the dragon. Amidst the destruction and chaos, the community and the circles of friendship within must rise again to face an uncertain future. The young scion of the Diamond Expanse Clan must now face his greatest threat as the forces of war build to a crescendo. With his friends by his side, together they will uncover forbidden mysteries and face off against ancient powers that have lain dormant for centuries.

This story is a sequel to School Daze

Cheerilee and Screwball expected a quiet Ponyville vacation. But Discord's back, and he's come for the children. Can Screwball and the Ponyville teens overcome the Lord of Misrule in their worst nightmares?

Twilight always thought that being able to send the Princess her letters instantaneously through Spike's fire breath was the best thing in the world. Instant correspondence with her mentor and secret crush could never be a bad thing, right? Unfortunately, Twilight has a habit of writing her secrets down on flammable materials. Now her secret's out, so what's a panicky unicorn to do? Panic, obviously!

Some things in this world happen by chance. Others do not. Twilight Sparkle is about to learn a disturbing truth that will turn her world upside down.

- Originally written May 2011 for Deviant Art

Reading this story first is strongly recommended:
(Blood is Thicker) http://ciroton.deviantart.com/gallery/26378692#/d3e1ndq

Credits:
~Image by JohnJoseco~ ~Edited by BrotherPrickle on Deviant Art~