Applejack groaned and opened her eyes. Before doing anything else, one hoof stretched out, grabbed her hat, and placed it on her head. Then she looked around, trying to see where she was and how she got there. She saw the ruins and suddenly it all came back. The Summer Sun Celebration. The Princesses disappearances. The appearance of Nightmare Moon. The inspector from Canterlot. The trip through the Everfree Forest. The ruined castle. The Elements of Harmony. The fight with Nightmare Moon. Then, the Elements glowing and the six of them floating in the air.

Applejack looked around again. This time she was looking for the mares she had came in with. She found four of them. Rarity, Rainbow Dash, Fluttershy, and Pinkie Pie were all laying near her. She could see them starting to show signs of waking up. But she couldn’t see Twilight Sparkle. Finally, she spotted the missing mare. She was standing near on the walls staring down at a shadow.

“Ya had me worried there, sugarcube,” Applejack said as she trotted over to the lone pony. “Last thing Ah remember was us fightin’ Nightmare Moon.”

Twilight didn’t say a word. She just stood there, staring down at the shadow. Applejack looked at the shadow as she approached the pony. In it, she could see the broken remains of Nightmare Moon’s armor. It was only then that Applejack noticed how unnaturally still Twilight was standing.

“Sugarcube? Twilight? Are you okay?” Applejack placed a hoof on Twilight’s shoulder.

And screamed.

Applejack scrambled back from the purple pony. She was waving the hoof she had touched Twilight with wildly. When she had touched Twilight, she had felt, things, moving under her skin. That feeling was creepy as buck. And it wasn’t something she wanted to repeat. Her screams of fright drew the others’ attention.

“Why are you screaming,” Rainbow asked as the group of mares rushed to Applejack’s side.

“Somethin’s wrong with Twilight,” Appplejack yelled as the others got to her. “Ah think Nightmare Moon’s inside her!”

“Whatever do you mean,” asked Rarity as Fluttershy squeaked and tried to hide behind her.

“Ah went up to her to see if she was okay,” Applejack explained. “When she didn’t answer, Ah touched her to get her attention. That’s when Ah felt it. It felt like somethin’ was movin’ under her skin!”

Fluttershy squeaked and tried to make herself smaller while the others gasped. Then Rainbow chuckled. “Good one, Applejack,” she said. “I didn’t know you had it in you.” She started walking toward Twilight. “How did you talk Twilight into doing this prank with you?”

“It ain’t a prank,” Applejack said. “Ther’ really is somethin’ movin’ under her skin.”

“Yeah, yeah,” Rainbow waved Applejack’s words off. “Now Twilight, I can appreciate a good prank. But enough is enough. This prank is over.” She placed a hoof on Twilight’s shoulder.

For one moment, nothing happened. Then Rainbow’s eyes shrank to pinpoints. She screamed and zipped back to the others. “There’s something moving under her skin,” she said as she shook the hoof she had touched Twilight with.

“That’s whut Ah been tryin’ to tell ya,” Applejack said. “It has to be Nightmare Moon. Somehow, she dun got into Twilight!””

“But the Elements of Harmony were supposed to defeat her,” cried Rarity. “How could she have gotten into Twilight while being struck by them?”

“Ah don’t know,” Applejack said. “But we gotta’ find a way ta get her out.”

Just then, there was a bright flash of golden light behind the group. Started, they turned to see what new threat was coming to them. Behind them stood two female ponies both had wings and a horn. One was a tall regal pony with a pristine white coat. Her mane and tail were the colors of the aurora and waved in a nonexistent wind. She was dressed in her golden regalia. Beside her stood a slightly smaller pony. This one had a dark blue coat. Her mane and tail depicted the night sky and also waved in a nonexistent wind.

“Princess Celestia! Princess Luna,” the group chorused before bowing.

“Rise, my little ponies,” Princess Celestia said with a motherly smile. “You should not be bowing to us. It is us should be bowing to you. You five have done Equestria an important service. Together, with Twilight Sparkle, you have saved us from a dire threat.” Celestia paused and looked around. “Where is Twilight?”

“Please don’t tell us she has been injured,” a worried Princess Luna asked. “It would not do for one such as her to be injured in her hour of glory!”

“We believe something worse has happened to her, Your Majesty,” Rarity said as she gracefully rose.

The two princesses looked at each other. “Where is she,” Princess Luna asked. “We need to confirm this.”

“Back that way,” Rainbow Dash said as she pointed at Twilight’s position. “She’s standing over a puddle of black goo.”

Princess Luna rushed to where the blue pegasus was pointing. Princess watched her sister rush off then turned to the others. “I’m sure it’s nothing serious,” she said. “Unfortunately, Twilight has had things like this happen to her before.”

“She’s had things moving under her skin before,” Rarity asked in shock.

Princes Celestia studied the ponies in front of her for a moment. On one hoof, what they were asking was a state secret. Only she, Luna, Twilight’s family, and a select few others knew this. On the other hoof, these ponies were now the Element Bearers. They were going to be involved in a lot of secrets. Whether they wanted to or not.

“What I’m about to tell you is a state secret,” Celestia told the group. “You are not to tell this to anypony else unless you have permission from either myself, my sister, Princess Cadenza, or Twilight. Can you promise me that?”

“Does this concern Twilight,” Rarity asked.

“Yes, it does,” Celestia solemnly said.

“Then I’ll do it,” Rarity answered. “I promise that I want tell another pony anything you say here.” She, and the others then went through an odd set of motions.

“Twilight is not a normal pony,” Celestia said.

“Well, duh,” the pink pony, Pinkie Pie, said. “She’s your student. Of course, she’s not a normal pony.”

“Pinkie,” hissed Rarity. “That’s not what she meant!”

“What did she mean,” Pinkie asked with a puzzled look on her face. “Any pony Princess Celestia takes has to be special.”

“All ponies are special,” Celestia said firmly, but kindly. “It’s just that Twilight is different.”

“I’ll say,” Rainbow Dash exclaimed. “Not every pony can fight evil like that!”

“Ah think the Solar and Lunar Guards would argue that,” Applejack said. “Especially the Lunar Guard. They’re the ones who fight along side Princess Luna! We Appples have a history of bein’ in the guard. My great, great grandpappy was a Solar Guard. And he was proud of it.”

“Sergeant Sour Apple,” Princess Celestia said with a smile. “I remember him well. He was up for many a promotion, but he never accepted anything past sergeant. Said he worked for a living. Then he apologized for implying that I didn’t work.”

“Yep,” chuckled Applejack. “That was Sour Apple.”

“That’s nice and all,” Rainbow said. “But what about Twilight? She will be okay, right? You said this happened before?”

“Yes, but not for some time,” Princess Celestia said. It was how we discovered that she wasn’t a normal pony.”

Before Celestia could day anything else, Princess Luna rushed up to the group. “Sister come quick,” she shouted. “You need to see this!”

“What is it Luna,” Princess Celestia asked.

“It is Twilight! Her clockworks have grown in complexity and have encompassed her entire body!”

“What?!” Celestia stared at her sister for a moment. Together they rushed to Twilight. Rarity, Applejack, Rainbow Dash, Pinkie Pie, and Fluttershy looked at each other for a moment before rushing to follow the princesses.

By the time the group had arrived, Princess Celestia had her horn lit and was examining Twilight. “My word,” the alabaster alicorn said. “They have spread all through her body!”

The five mares, hearing this, looked at each other. After a moment, Applejack stepped forward. “Beggin’ your pardon, Princess,” she began. “But what has spread through Twilight’s body?”

Princess Luna looked at the five ponies. Then she looked at her sister. “She has not told you,” Luna asked as she turned back to the ponies.

“We kept getting kind of side-tracked,” Rainbow Dash said while rubbing the back of her head. “She did mention that Twilight was different.”

“That is one way of putting it,” Princess Luna said. She cleared her throat. “For some reason, which we cannot fathom, some of Twilight Sparkle’s skeleton is made of metal. Specifically, her spine, half her skull, and eight ribs.”

The five ponies gasp. “Oh my,” Fluttershy said. “Was she in some sort of accident?”

“We do not know,” Luna said. “Additionally, several of her organs have been replaced by machines. And there are incredibly thin strands of some time of wire running through her nervous system. It even taps into her thaumic channels.”

All five of the ponies had wide bulging eyes and looks of horror on their faces. “My goodness,” Rarity exclaimed. “How is she still alive?”

“How is that even possible,” Fluttershy asked. “None of what you said is even medically possible! When did this happen to the poor mare?”

Princess Luna sighed. “That’s the problem. We don’t know. After Twilight was accepted into the Royal School for Gifted Ponies, she was given a medical exam. All students are. That was when we found the metal bones and mechanical organs. There was nothing in her medial files that even hinted that they were there. Even her parents were shocked. The only thing they could point at was a strange illness that she came down with a month before her exam. But she recovered from that in a day.”

“Even now,” Luna continued. “We don’t know who, how or why this has happened. But we are monitoring the situation. We have the best doctors and scientists working with Twilight. Not to mention my sister. Between them, they will be able to figure this out.”

“But why is she just standing there,” Rainbow Dash asked. “She is alright, isn’t she?”

“She is perfectly fine, as far as we can tell,” Luna said. “She has been like this before. We did ask her what was wrong at those times. Twilight just said that sometimes, the machines inside her need to reset. When they do, she just stops.” Luna turned to look at Celestia and Twilight. “On some level, she is aware of what’s around her. Enough that she can react to dangers.”

“So she is okay,” Applejack asked.

“Yes,” confirmed Princess Luna. “We just need to wait for her to wake up.”

“But what about the changes you mentioned,” Fluttershy asked.

“That’s why we need to wait. She’s the only one who can tell us what those changes mean.”

“Oh. Okay,” Fluttershy softly said.

“Do you know how long it will be,” Rainbow Dash asked.

“Rainbow Dash,” Rarity exclaimed.

“What,” the blue pegasus asked. “I want to know.”

Luna laughed. “Patience,” she said. “I too want to know, but there is no rushing this. We do not know much about the things in Twilight. Rushing them could cause serious problems for her.”

“We don’t want to do that,” agreed Fluttershy.

“But I want to know,” Rainbow Dash shouted. “She sounds like a Robomare.”

“Robo-what,” Applejack asked.

“Robomare,” Rainbow repeated. “You know, half robot, half mare.”

“Are ya talking about one of those there comic books Apple Bloom reads?”

“Yes,” Rainbow excitedly answered. She turned to Princess Luna. “Is Twilight like Robomare? Is she stronger than a hundred stallions?”

“Ooh, ooh,” Pinkie excitedly jumped in. “Can she shoot lasers out of her eyes?”

Luna laughed. “She can’t do those things. Although, she is the inspiration for Robomare. Ten percent of the sales goes to her.”

“That’s so awesome,” Rainbow shouted. “Now she has to wake up! She has to tell me how she started Robomare.”

While her sister, Luna, was talking with the ponies, Princess Celestia was examining Twilight. Celestia would be the first to admit that her sister was better when it came to modern devices. Even the most complicated of clockworks. But between the two of them, Celestia was the one who knew Twilight and her inner workings the best. After all, Twilight was her personal student.

As she examined Twilight, Celestia could see that Luna had told her the truth. In fact, it seemed that she had under-stated the changes Twilight had undergone. Her entire skeleton was now composed of metal. Her muscles now had pieces of machines running through them. Mostly pistons, gears and pulleys, it seemed. The impossibly thin wires now ran through her entire nervous system instead of just being in her spine and brain. And the mechanical devices. They were everywhere! There wasn’t a single organ that did not have, at least, one device embedded in it. Some were replaced entirely and had only a thin covering of tissue. Others were laced with them.

Also, there appeared to crystal formations spread all through her body. Celestia couldn’t determine why they were there. But she could tell they were there for a reason. She could detect magic radiating from them. From what she knew of magic, she knew that wasn’t by accident. Tracing their flow of magic led the alabaster princess to a metal and crystal device located in Twilight’s head at the base of her horn. This was not there the last time she had looked. She wondered if the scientist knew about it. Or the doctors. Did Twilight know? Worried by this find, Celestia started looking for more similar changes.

She found them.

Replacing Twilight’s heart, Celestia found a strange pump. This pump not only moved Twilight’s blood; it also propelled a strange energy throughout Twilight’s body. It was an energy that Celestia did not recognized. It wasn’t thaumic in nature. Nor was it electricity. All of the strange machines and devices seemed to run on this energy. And now that she was looking, Twilight’s body seemed strangely dense. Like there was more, a lot more, to it than could be seen. And she could detect no signs of spatial folding.

Celestia knew that the scientist and doctors would have a field day studying the changes in Twilight’s body. Of course, Twilight would be the most excited of all. But this was not something to get excited about. It was something to be worried about. She was sure Luna would agree with her. The Changes in Twilight were beyond what she had though possible. At this point, Twilight seemed to be more machine than pony.

Suddenly energy pulsed through Twilight. The machines and devises started activating throughout the young unicorn’s body. It seemed that Twilight was waking up. “Sister,” Celestia called out. “I believe that Twilight is about to wake.”

Author's Note

And here's chapter 1. I want to thank you for reading this so far. Hopefully I haven't disappointed you. I tried to establish some major differences in this story. How these, and future, changes came about will have to wait for future chapters.

Remember, I am a hobby writer. I write for my enjoyment.