The sun was setting, causing the clouds to be set into a pastiche of numerous firey colors. If Twilight Sparkle didn't know any better, she would think that dragons were upon the clouds, setting them ablaze. The orangey wisps were upon the edges of the clouds, beginning to drift away. Twilight turned to the Apples, who had finished their work for the day; Twilight participated in a long, and hard harvest of apples, as Applejack was her best friend, and she couldn't help but admit to herself that she found Big Mac kind of, well, attractive to her. There was something mysterious about that stallion. They were now all far away from each other, and they had been carrying the last of their pickings, gradually converging towards the barn. In particular, she observed Granny Smith. Granny Smith wore a saddle, with an apple basket on each side, and yet, she seemed to be limping - not a surprise, for some reason her own grandchildren set similar expectations for her to themselves, didn't anybody ever tell them to respect their elders? - but her face was unusually...forlorn.
And that was a surprise.
Twilight trotted right up to her, just to see if there was anything she could do to help her. The barn door was in sight, after all. If she could just help Granny Smith carry those apples all the way to it...it shouldn't be too hard, right?
"Granny, please, let me carry those basket for you!" Twilight demanded.
Granny Smith brushed off the offer with a wave of her foreleg. "Oh, that would be just swell Twilight, but I don't need it!"
Twilight's eyes narrowed. "Uh-huh. Your limp disagrees."
"Oh, that? Why, this body is simply getting too old to keep going" she said with a slightly happier face.
The fact that her tone and expression cleared disturbed Twilight to no end. "Granny, don't speak of death like that!"
Granny Smith almost seemed...surprised. If not offended. "Oh pooh, who said anything about dyin'?"
Almost ironically immediately after she said that, she began to wobble, and fell to the ground.
"Granny Smith!" Twilight shouted. She was worried, was she going to die? Twilight took things into her own hooves: She grabbed Granny by the nape of her neck, and dragged her to the barn. But as soon as Twilight began to let her go, something happened:
First, Granny Smith began to glow; then, her face became...distorted. The mouth twisted and turned, and soon, the entire head began to look like a slowly metamorphosing picasso, which now looked like it was constantly being metamorphosed back and fourth by a child's hands.
Then it stopped. Her body stabilized.
But it no longer looked like Granny Smith. She now had a beige coat, a crimson mane...and her body was a lot younger. Almost Twilight's age, in fact.
Twilight turned around, and saw that the other Apples were standing at the barn door entrance. How long were they standing there? Applejack gently cradled the pony who was Granny Smith: "Oh, it's okay darlin', it's just your first regeneration." Twilight gaped at the very everyday response to such an abnormal phenomenon. Big Mac looked and Twilight, and then back at Applejack, and said to her: "I'll deal with her."
Twilight, was still, wordless. Big Mac walked to her the house next to their barn, and now he had spent the past two minutes nervously pacing around the couch she sat on. Then he paused. With a sigh, he made a decision, and decided to sit down on the loveseat in front of Twilight. Once again, there was a silence, and a pause. Nobody said anything, anything at all. It felt like eons, though it was most probably merely minutes, if not seconds.
Finally, Big Mac spoke:
"I think it's time to drop the charade. We're not who you ever thought we were."
"Yeah, I gathered that" Twilight answered blankly, still incapable of knowing what to make of this.
Big Mac simply grunted under his breath and kept talking, slowly, as if Twilight might not be able to understand. "Applejack and I aren't siblings. Granny Smith is not our grandmother, and Apple Bloom is not our sister."
Twilight merely cocked an eyebrow at this; for one thing, she previously depended her entire understanding of the Apple family on the very assumptions that Big Mac refuted, and for another thing, she never heard Big Mac speak in such a long and complete sentence before. "So, none of you guys are related?"
"Oh, we all are, just not AJ and me, but Smith and Bloom are both related to us."
Twilight still didn't understand, but she sat up, wide-eyed and alert, to take in everything.
Big Mac wasn't sure how to take explain everything, and with a frustrated facepalm at himself for not being more direct, he began to explain: "Applejack is my wife."
Twilight almost giggled at this, but remembered what he said before. "So, if AJ's your wife, that means that Apple Bloom is your daughter?"
"EeYup!"
"But how can Granny Smith be related to both of you, but you and AJ aren't related to each other? I don't understand-"
Big Mac hardly needed to hear anymore: "Because 'Granny Smith' is our elder daughter; she was merely nearing the end of her first incarnation."
Twilight Sparkle thought that she heard enough. "Okay, I'm going to call some nice people in white coats-"
Big Mac, however, put his hooves on her shoulders: "Twilight, you must believe me: We're not of your people, and not of this planet."
Twilight weakened and began to sink to the couch again.
Big Mac sat back down and explained. "We come from the planet Gallopfrey."
Twilight tried to believe this...somehow, she couldn't.
Big Mac seemed to be spending time, thinking about what to say. His ears perked up, as if an idea burst into his head. "Twilight, did you ever feel our heartsbeat?"
"Heartsbeats?" Twilight asked, utterly confused.
Big Mac nodded a little more cheerfully. "Put your hooves on my chest."
Twilight was slightly hesitant, but she placed one hoof on each of his pectorals - he was inredibly strong and firm - and she put her head against his chest, one ear on his body. She listened and felt carefully...
...Then she saw what he was talking about.
She got her hooves off of his body, and her face moved back several inches. "You have two hearts!"
A small smile creased Big Mac's face. "Eeyup!"
Twilight leaned back further, trying to figure out what to ask; she had so many questions on her mind. "So, um, what happened to Granny Smith?"
He explained in the most matter-of-fact tone. "Why, a biological transdifferentiation; the mRNA signaled to the DNA of each cell to lock genes that were previously used and unlock genes that previously weren't; the process also happens to rejuvenate one who undergoes it. Granny simply became too old, and cell after cell signaled to another to change. I've already burned through four bodies; this is my fifth incarnation. Does that make sense?"
Tqilight simply looked confused. "Who are you really?"
Big Mac decided to sit back and explain. "On my home planet, I specialized in the cosmic sciences, namely temporal research. I was once given special permission to examine how small decisions could influence the rest of history. ...Oh, I neglected to mention, my true name is Magnus."
"Magnus...do all the other ponies go by pseudonyms?"
"EeYup!"
Twight trembled further "And you said that...You- you're a Time traveler? How?"
Big Mac, or I should say, Magnus, immediately understood what was wrong. "Ah, I neglected to tell you, I'm not just an alien, I'm not exactly your average Gallopfreyan...I'm a Time Lord. I bear an academic rank granted to me by the Prydonian academy that permits me to study the entirety of the cosmos by means of time travel; in other words, I proudly bear the rank of 'Master'; few from Gallopfrey can top that."
"Yes," Twilight said, "but how do you actually do it?"
"Oh, that? I simply travel by TARDIS, that's short for "Traversible Acrhonal Retrograde Domains In Spacetime", and that's our current home and means of transportation, it's disguised as a house; you're sitting in it."
Twilight looked down nervously. Magnus chuckled. "It's an object that is composed of, encompasses, and exists in more dimensions, than the traditional three. With it, I can go wherever and whenever I so desire, and from there, the rest is easy, just enough intervening with the lives of others, and I can change the entire course of history. I was one of the few with the credentials to actually be present in particularly critical points in place and time for our history. I could study, and with the right passes given to me, I could intervene as I saw fit."
Twilight was now nothing but fascinated at this stallion, whom she knew as Big Mac, but was really named Magnus. "Why?" she asked with a whisper.
"Because, I see a Universe. I see suffering and folly in it. As somebody with the power to make things right, I feel that it's my responsibility to do so. Think bout how different things would be, if people had better medicine and understandings of biology and astronomy sooner, or if that one horrible book was never published, or if child who grew up to be the ruthless dictator was never even born. " Twilight felt a chill after hearing that last remark. Magnus kept going: "But now...I can't. I was - well, I guess you could say I was downsized." Magnus now blew out a sigh of disappointment and defeat.
"How come?" Twilight asked.
"Well, there was this guy, a very important Time Lord named Morbius. He decided to interfere with critical points of history to first build up a cult of personality, and then overthrow Gallopfreyan society. So they put rules against 'meddling', as they so put it, with time."
It clicked with Twilight: "You're a time meddler!!"
Big Mac shook his head. "No, I'm a time-renovator. I sort the messes and the kinks out from it. I can't just look at our horribly arranged Universe and let it remain the way it was. As a Time Lord, I have a responsibility to the many who could suffer, if only one little thing was different, if only that one person didn't die...or if only that one person did."
Twilight wasn't sure what to make of that, and decided to simply listen to what else he had to say: "So what do you do now?"
"Now? I tried to lead a protest to the academy to get my job back; there was no way they would take my job away from me ; they wouldn't listen. Now I'm a wanted criminal."
"So, you're a fugitive? Why are you on this planet?"
"Because I've got nothing left, no family, no friends, even my own half-brother, who supported most of my endeavors, thinks that my revolution was going to far...but I can regroup here. This planet has some of the best resources available to us. Namely it's own people-"
Another question popped into Twilight's mind: "And what about all those other Apples? Are they also from Gallopfrey?"
Magnus smiled: "I was getting to that. No, none of them are related to us. However, we convinced them with our telepathic amplifier equipped in our TARDIS that they were related to us. It made it easier to snag them one by one..."
"For what?" Twilight asked with wide eyes.
Magnus spoke on, eerily cheerfully. "To gradually break down their minds, and create perfect, unquestioning soldier out of them. With them, we can overthrow the High Council on Gallopfrey, and then use them to police the Universe. I've already allied myself with the War Lords - we'll test our troops on a War Zone planet, before we use them."
Twilight nervously chuckled. "Well, um, that's...very interesting. However, can't you just go back in time and prevent that from all happening? I mean, your plan sounds a little bit like what that Morbid guy did."
A control console had rose from the living room floor, and Magnus turned a lever on it. He went back to talking. "Morbius? That idiot wanted power. I merely desire perfection. Anyway, I tried to go back in time to fix things, but the other Time Lords are using their transdimensional engineering skills to prevent me from tampering with what they consider should be "fixed points in time". I either can't meddle with it or only can by means of scarring the Universe. Not pretty. I have no choice but to undo their barriers with sheer force. I want to ask you this; will you join us? Out of all the savages on this planet, you always struck us as the most intelligent. We can give you say over the general direction of this Universe. Are you with the Cause?"
Twilight nervously chuckled again, "Well, I'm very interested in your plans for hypnotizing ponies into ensuring Universal domination, no, really, I am, but I have to get going, lots of important things to do to tomorrow! Um, talk to you later!"
Magnus, however, knew insincerity when he heard it. "Then you leave me no choice." Twilight saw that Magnus was now at the medicine cabinet, with a cloth in one hoof, and grabbing a chloroform bottle by the handle with his mouth.
Oh my Sunflare, Twilight thought. She knew what that meant: She galloped for the door, trying to pry it open - but somehow, it was locked, although there was no visible lock set on it. She turned around, and saw Magnus behind her, and Twilight, now weak with fear, slowly collapsed to the floor. "I got the console so I could take the precaution to lock the door, in case you got...cold hooves" he explained.
His eyes looked sad, but she could see there was no way of stopping him. "I'm sorry Twilight, but this will hurt me inside far more than it will hurt you in body." He grabbed her in a headlock, and shoved the cloroform smothered cloth over her face. Twilight struggled, driven by the vague hope that she might be able to be break free, but Magnus was very strong, and the chloroform was making its way through her respiratory system, causing her great pain.
Finally, losing the will to live, Twilight collapsed on the floor, unmoving.
Applejack came though the back door, and now she was looking at Twilight, and then she looked at Magnus. "Is she...?"
"Yes" he answered sadly. "I tried to get her to join us, but she- she wouldn't-"
Applejack put a sympathetic hoof on his shoulder. "It's okay honey-bun. Still..." she added with a sigh, turning back to Twilight, "it's an incredible shame that she never got to be on our side. She was my favorite native around here."
Mgnus nodded sadly "EeYup."
Applejacked asked with a grave voice: "So, what do we do with the body?"
He paused and thought about it. "We'll take it with us on our TARDIS, find a remote place in space and time, and dump it there....Twilight was important to this community, we're going to have to make a run for it, and not look back; hopefully, without TARDIS memory-tampering presence, they'll forget we were even there. Did you get the kids?" Applejack nodded. "This the fourth time this has happened; of course I got the kids." Magnus gave a curt nod in reply. "Let's go then." He touched a switch on the TARDIS console, and their house began to move with a screeching groan, ready to go through time and space.
Several hours had passed as Magnus was seeking out a place to put the body, and Apple Bloom looked out the window sadly, her eyes almost teary. "What's wrong Apple Bloom?"
"Ah have friends back there, friends who weren't easy for me to make...but without the TARDIS in Ponyville...they're all gonna forget ah existed!"
Big Mac gently patted her on the back: "Well, think about it this way...we're going on an adventure!"
That hardly cheered up Apple Bloom at all. She dived her head into his chest and wept.
"Shhh, It's okay my little bird," he whispered, trying to be comforting "it will soon be over, and then, and then, we can settle, and live a normal life, with friends and family."
Big Mac suddenly felt some kind of pounding his head, a pattern of pounds like this:
One-two-three-four!
One-two-three-four!
One-two-three-four!
One-two-three-four!
Applejack turned around: "Magnus, Honey, are you okay?"
"Ye- yeah. It's just this...pounding in my head."
Applejack gently embraced Big Mac: "Aw, it'll go away darlin'!" She ended her statement with kiss on his muzzle.
Magnus could only hope so; the drums were calling him, calling him to something...
...Calling him to war.
Author's Note
This is the physical appearance of Applejack's previous incarnation, and it's very similar to Granny Smith's new incarnation. 
Yes, it's Granny Smith's mother from Family Appreciation Day.
Yes, I totally implied that Big Mac was to eventually become the War Chief, and later the Master. Obviously, something happened to his family to finalize the change that had been mounting for a long time...
I got the idea of the overall concept from this:
An entry for LyraAlluse's Random Fiction contest.