Crossover. However, I just take the basic idea of the video game and transform it. Playing the game yields no spoilers whatsoever. Meaning, you don't have to have played the game to understand this story.
Pinkie Pie is the Priestess of Regeneration: she has to go on a dangerous quest to heal the world, so says the Princess Goddess Celestia. She will be accompanied by her teacher, crystal pony Twilight Sparkle, and the mercenary knight Captain Spitfire. She will need protection from the Desians (a mixed-blood race of half crystal pony, half non-crystal pony) who wish to continue the scarring of Equestria, as well as the monsters who guard each Element of Harmony. There are six elements, and all are required to unlock the path to a tower built by the crystal ponies: the Tower of Harmony.
However, the quest gets complicated. Pinkie Pie's best friends Rainbow Dash and Trixie Lulamoon (Twilight's younger sister), through a cruel twist of fate are banished from their home village because they'd accidentally initiated an attack by the Desians. And, what's more, the five encounter a global conspiracy. The Exspheres, crystals that give you great power necessary to collect the Elements of Harmony, are actually made by draining the love and happiness out of ponies, ultimately killing them.
On top of that, they find that there is another whole world they didn't know existed. An assassin who had been trying to kill the Priestess, Fluttershy, turns out to be a protagonist, who wanted only to protect her own world. They find a second priestess of this other world, Rarity. And two more ponies whose lives were destroyed by Exsphere research: Applejack- one whose eyes contain no life- and 'Big' Macintosh- one who binds himself because of a past sin.
The one ultimately responsible for all the suffering is Night Mare Moon, the grieving sister of the Goddess who sleeps, Celestia. Can the ragtag protagonists convince Nightmare to redeem herself for all her wrongdoings? [Summary will be refined as the story is written]
Rated T for violence and moderate shipping*.
Featuring:
Martel- Celestia
Lloyd- Rainbow Dash
Colette- Pinkie Pie
Raine- Twilight Sparkle
Genis- Trixie Lulamoon
Kratos- Captain Spitfire
Sheena- Fluttershy
Zelos- Rarity
Presea- Applejack
Regal- Big Macintosh
Yuan- Discord
Botta- Gilda
Altessa- Zecora
and
Tabatha- Derpy
Ships are PinkieDash & RariShy (MacJack would be Squicky)