In the quest to save the two weakening alicorns, Twilight and Sunset will travel across Equestria and even into the Princesses' past to get the answers they need.

Everyone will have to fight to save their home as they know it from creatures of darkness that are growing ever stronger and will try anything to stop Luna and Celestia from reawakening.

In the world of Pokémon and Ponies two young fillies will meet at a large castle and become great friends but they will be torn apart by evil. One of them will help to save the world of Ponies and Pokémon from the evil group known as Team Plasma that is trying to take over the world by controlling the Heroines to do so. What will happen if she can not save the world she loves and what will happen when an old friend comes back that she forgot about. Well read the story to find out .

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Ponies Playing the Pokémon Trainers and others

Hilda / Touko / White - Played by Princess Twilight Sparkle
Lord or Prince N - Played by Princess Luna
Hilda's Mother / Touko's Mother / White's Mother / Annabel - Played by Twilight Velvet
Cheren - Played by AppleJack
Bianca - Played by Pinkie Pie
Touya / Hilbert / Black - Played by Rainbow Dash
Professor Juniper ( Female ) - Played by Fluttershy
Female Runner - Played by Rarity
Ghetsis - Played by Nightmare Moon
Concordia - Played by Princess Celestia
Anthea - Played by Princess Cadence
Sage Zinzolin - Played by Starlight Glimmer
Sage Ryoku - Played by King Sombra
Sage Giallo - Played by Queen Chrysalis
Sage Rood - Played by Discord
Sage Bronius - Played by Lord Tirek
Sage Gorm - Played by The Tantabus

Ponies Playing the Pokémon

Purrloin / Liepard - Played by Shining Armor

Twilight's Pokémon

Pidove - Played by Scootaloo
Snivy / Servine - Played by Moondancer
Zorua - Played by Sweetiebell
Deerling - Shiny - Played by Applebloom
Axew - Played by Spike
Blitzle / Zebstrika - Played by Sunset Shimmer

Rainbow Dash's Pokémon

Oshawott - Played by Tank

Pinkie Pie's Pokémon

Tepig - Played by Cherry Jubilee
Munna - Played by Prince Rutherford

Applejack's Pokémon

Snivy - (No Name)

There will be a lot more Pokémon and will add who is playing them when they come in new chapters.
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Places

Canterlot
Fillydelphia
Ponyville - Gym - Gym Leader Big Mac
Las Pegasus - Gym - Gym Leader Daring Do
Baltmare - Gym - Gym Leader Nightingale
Crystal Cave
Celestial Tower
Sun Touch Bridge
Moor of the Moon

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The Cover Art is not mine and I do not know who it belongs to but it is great a great picture.

My Little Pony Friendship is Magic Characters are owned by Hasbro and Lauren Faust.

Pokémon characters are owned by Nintendo and Game Freak.

I own nothing but this story I write.

Once upon a time, far away there was a magical land named Equestria. In it, there lived five mares named the ‘Guardians of Equestria. They protect ponykind and are loyal defenders of Princess Celestia and Princess Luna, the rulers of Equestria .
Applejack, represents the Element of honesty. Fluttershy, is the Element of kindness. Rainbow Dash, Element of loyalty. Rarity, Element of generosity. And Pinkie Pie, Element of Laughter.
Together with the princesses, they have kept Equestria at peace for years.

However one faithful day, the Guardians are stripped from their status for no apparent reason and have been removed of honoring the Elements.
Rumors spread. Ponies believe that the Guardians have done something atrocious to be removed of such importance. They now have almost the entire population chasing their tails for a crime they did not know they committed. They manage to escape and leave Equestria, as it is not safe for them anymore; They are on a journey to the Crystal Empire, a kingdom where a third princess lives, one of their closest and dearest friends. There, they are safe from the dangers in Equestria. On the way they encounter a pony who has never been permitted outside of her village but wishes to explore the world. the pony, Radiant Night decides to join the guardians on their travel to the Crystal Empire. However, Radiant Night soon finds out that perhaps meeting the guardians wasn't out of luck, and there's more to the story than she thinks...

Two years after Nyx was stripped of the Nightmare's power, Twilight Sparkle is attempting to raise Nyx as a normal filly. But as Nyx's magical abilities begin to grow out of her control, the pair quickly earn the attention and ire of some powerful ponies who do not have Nyx's best interests in-mind.

During the night, the Elements of Harmony mysteriously vanish, and Princess Celestia enlists the aid of their bearers to find them. Twilight is forced to choose between her duties to her princess and her duties to her daughter. In the process, she discovers a web of conspiracy surrounding her daughter that reaches back a thousand years into Equestrian history. Will Twilight be prepared to face the things she learns along her journey's path: about Nyx, about Celestia, about Equestria, about the Elements...

...about herself?

Based on Past Sins by Pen Stroke Pony.
Alternate universe, because Twilight never became an alicorn or princess in this story.

Far, far away from the Equiss system, the queen of blades is readying the launch of her newest weapon. A ship designed to infest an entire planet in secret, readying it for the eventual zerg invasion and softening up even the hardest target, Korhal. Unfortunately for the queen of blades, the untested zerg biotechnology is more difficult to master then she thought and the infestation ship vanishes after launch.

Untold eons later Twilight Sparkle is preparing for her entrance exam for Celestia's school for gifted unicorns only to stop when she sees a star fall into her new treehouse. The young pony sets out in the middle of a storm, intent on seeing this fallen star for herself.

What she finds inside will change not only her destiny but the destiny of all on Equiss prime.

Make sure to check out the sister story to this one.
Trigger warning, parasites. Starcraft Crossover!
Updates twice a month!
The story so far!

It's been a year now since Twilight vanished after attempting a sonic rainboom. She's spent her time fighting in WWII alongside her brothers in arms. Now, after a bad jump, she finds herself back in Equestria. After a well deserved rest, a nice, warm bath, and the most unusual breakfast, she begins to tell her story.

Twilight Sparkle, Princess and now mentor to Starlight Glimmer is having a great time at a party Starlight is throwing. After the party everything starts to snowball into chaos. As the cutie map summons everypony to it; all confused to the reason why the map needed them all the mane six look at each other. Till each one starts vanishing to the far reaches of Equestria, all but Twilight.

Can Twilight get her friends back before Equestria is destroyed by the princesses and Discord. Can Twilight even stop the pony behind it all or will Equestria fall into eternal chaos because of this pony.

Join Twilight on this endeavor to see if she fails in the quest at hand or over comes it.

It has been one year since Starlight Glimmer graduated and ventured out on her own to teach others the friendship lessons she learned as Princess Twilight's personal student. Now, unexpectedly, she's coming back to Ponyville for a visit, and everypony is excited about it. Well, everypony that is, except Spike. But why?

Twilight, Fluttershy, Dash, and Rarity have gotten trapped in final fantasy 1 and have no idea how to get back home. Join them on an epic quest to find there way home. Full of fun, danger, and new friends of all kind.

A story of a future generation, set in the Order-naries 'verse.
Reading the previous stories is not necessary.

Peace, Friendship, and Harmony reign supreme across Equestria and the wider world. An entire generation has grown up not knowing firsthand the terror of villains like Nightmare Moon, Tirek, and Grogar. Members of every species can travel, live, and thrive in any place they so desire, and what few problems that arise are easily dealt with by local leaders. In short, everything is perfect.
And Princess Twilight Sparkle, Alicorn of Friendship, the pony responsible for it all, is bored and depressed. Her moodiness affects her two personal students in magic, Bellatrix Lulamoon and Citrine, daughter of Rarity and Ashen Blaze, causing the two to bicker and fight instead of building a friendship.
In a desperate bid for direction, Twilight consults the long-silent Cutie Map, which sends her on a short walk to a big revelation:
Thanks to Twilight, Equestria can handle its own home-grown problems, but new threats of unknown origin approach the peaceful world. To aid the land through a new era of danger and growth, the spirit of Harmony magic itself is forging a new set of Elements, and it will be Twilight's job to find and prepare six new Bearers to take them up, define their virtues, and face the Intruders.

Little does any creature know just how soon the new Elements will be needed.