A New Harmony

by The-rogue-shadow


Chapter 1

Twilight cast the spell on Applejack, merging her mind with that of the comatose Pegasus Rainbow Dash, in an effort to wake up Rainbow from her coma. The coma was a result of a brutal attack by Rainbow's former friend Gilda, the griffin. Twilight slumped down, exhausted from the effort of casting such a difficult spell. Fluttershy flew over and helped her up.
"Are you okay Twilight?" Asked the timid yellow Pegasus, Twilight nodded to indicate that she was okay. The others that had gathered in Rainbow's hospital room breathed a sigh of relief. Twilight's friends had all gathered to give Twilight support; there was Fluttershy, The white Unicorn Rarity, the pink earth pony Pinkie Pie and Applejack's Brother and Fluttershy's coltfriend Big Mackintosh.
"So what do we do now Twi." Asked Big Mac, his voice full of concern for his little sister, Fluttershy flew over and hugged him.
"We do the only thing we can; we wait." Said Twilight, she had originally intended to go into Rainbow's mind to retrieve Rainbow, but was talked out of it by Applejack, who had insisted to go instead.
"Unfortunately Twilight, we cannot even do that." Said a voice behind them, Twilight looked up at the beautiful white Alicorn Princess Celestia, ruler of Equestria and Twilight's mentor. The look on the Princess' face was a mixture of sadness and anger.
"Princess Celestia!" Twilight exclaimed, the ponies all bowed in respect to the Princess.
"Yes Twilight, and I'm sorry but we have no time for pleasantries, the very fate of Equestria is at risk." Said Princess Celestia, her voice was filled with a seriousness that Twilight had never heard before.
"What's the matter Princess?" Inquired Twilight, beginning to get worried.
"You remember the Griffin that attacked Rainbow Dash?" She asked, and continued her explanation at the looks of anger that came across the faces of the ponies. "Well she was not just some random griffin, unbeknownst to me; she is the daughter of the leader of the United Griffin Empire." The ponies gathered around Celestia all gasped, Rarity was the most dramatic; she feigned a faint as she gasped. "And that is not all, because of the actions of Big Mac; they have declared war on Equestria, effective immediately."
"WHAT! Ah was only protecting my sister, from that so-called Princess." Yelled Big Mac.
"That may be so, but whatever story she told, it has gotten her father angry enough to break the truce between our nations that has lasted six hundred years." Said the Princess, looking sympathetically at Big Mac.
"Is there any sort of peaceful solution?" Asked Fluttershy, hiding behind Big Mac.
"I'm afraid not Fluttershy, they are refusing every offer of peace that we make with them." Celestia replied.
"So what do you want us to do Princess?" Asked Twilight, suddenly becoming very serious.
"I need you and the other elements to take up arms against this threat and defend Equestria." Proclaimed Celestia, invoking a strange feeling of pride in the ponies.

"Yay! Let's go get those big Meany griffins." Said Pinkie Pie, jumping around, she suddenly stopped in mid-air.
"Wait, I just remembered, we're down two elements." She said, looking at her two bed ridden friends.
"Then we will have to find replacements." Said Twilight, to which Celestia nodded.
"Can you think of any ponies that embody the elements of honesty and loyalty?"
"What about Big Mac, he's very honest, and he's the bravest pony I've ever met." Said Fluttershy, suddenly coming out from her hiding space and kissing Big Mac on the cheek, making him blush.
"Ah'd love to darlin, but ah don't think that I could handle the pressure of being an element, I'm not honest enough. Ah will gladly and easily lie to protect people ah love. But make no mistake, ah will gladly fight for you princess." Big Mac said, turning and kissing Fluttershy, whispering his apologies into her ear. He then turned back to Princess Celestia;
"But ah have heard tell of a pony who is meant to be the most loyal in history. They say that he is not only loyal to Equestria, but to the whole planet."
"And I know a pony who has never ever lied, not once, she's a bit clumsy, but she's always willing to help." Smiled Pinkie Pie. Princess Celestia nodded and smiled,.
"I know exactly the two ponies you mean." She bowed her head, concentrating as her horn began to glow white. A sphere of white appeared in the middle of the group, and dissipated, leaving two stunned looking ponies in between them. One was a brown earth pony, a stallion, his coat, mane and tail were all brown, and his cutie mark was an hourglass. The other was a grey Pegasus, whose mane and tail were blond, and was fairly pretty, the only thing that seemed strange was her golden eyes, they looked in different directions.
"What the hay? How did we get here Derpy? The last thing I remember, we were in the Tar-." Said the brown pony, before Derpy interrupted;
"Doctor, look! It's Princess Celestia!" She said, smiling an enormous smile.
"Oh My, Hello Tia." Said the Doctor, Twilight's eyes widened as the Doctor jumped up and gave Celestia a kiss on the cheek.
'Oh my Celestia, who is this pony?" Thought Twilight.
"Hello Doctor, it's good to see you again." Smiled Celestia, obviously the two had a history together.
"Same to you Tia, wow, it must have been what, a few centuries at least." Said the Doctor cryptically.
"Just who in the Hay are you?" Asked twilight, fed up with wasting time. The Doctor looked at her and his eyes widened, as though he hadn't noticed the other ponies that had gathered.
'Oh, I'm sorry, hello, I'm the Doctor." He said, before walking over to the sleeping forms of Applejack and Rainbow Dash.
"And what's this? The Rainbow one's obviously in a coma, but what's with the orange one, sleeping, no, then what would be the reason for the spell." He bent down and licked Applejack's face, making the other ponies cringe. The Doctor stuck his tongue out;
"Ugh, sour, new spell huh? First time trying it, hm, OH! I know, you have merged the minds of these two ponies so as to make the Rainbow one wake up, brilliant, absolutely brilliant." The Doctor chuckled to himself as Twilight's mouth dropped open.

"Yes, tha..that's right. It will last for two days before Applejack is trapped or is pulled back into her own body." Said Twilight, stammering for words as she explained. The Doctor smiled at Twilight and said;
"I see, well then, I suppose I should help out then shouldn't I?" He placed his hooves on either side of Rainbow's and closed his eyes. After a moment, he pulled his hooves away and walked back over to Derpy.
"And just what did you just do to Rainbow Dash, you strange stallion?" Asked Rarity, staring at the Doctor, a gleam of lust in her eyes.
"I did something very simple, I planted a seed." He said, before turning and making his way for the door.
"A seed?" Asked Fluttershy, suddenly interested if there was plants involved.
"Yep, a seed of doubt." He said and began to walk out of the room, Derpy following closely. The group, including Celestia all looked at each other, a look of confusion and shock on their faces, then turned back, before realising that the Doctor was leaving. As one voice they all called out his name, beckoning him back.
"What, wasn't that what you wanted me for? To help wake up the Rainbow one?" He asked. Celestia gave a sigh, remembering what a handful the Doctor could be.
"No Doctor, we need your help in defending Equestria from a war with the griffins."
"OH… what do you need me to do?" The Doctor smiled awkwardly.
"We need you both to stand in for these two as the elements of Loyalty and honesty respectively." Said Twilight, absolutely stupefied at the Doctor. The Doctor looked at Derpy, who was staring daggers at Rarity.
"So what do you think assistant? Ready for another adventure?" He asked her, Derpy looked back at him and smiled;
"With you Doctor? Always."