Derpy rolled over for the seventh time in the last half hour. She sat up and opened her eyes.

It was still mostly dark in the room. In the far corner there was a candle burning and also a very blurry shape. She blinked a few times and it came into focus. It was the Doctor reading a book by the candle's light. He wasn't speed reading, as he normally did, but read at a relatively normal pace.

The Doctor glanced up from his book and looked at Derpy, then went back to reading.

"Trouble sleeping, Derpy?" he asked, turning a page.

"Yeah," Derpy rubbed her eyes, "I just can't stop thinking about Pinkie Pi- I mean Dinky."

"It's norm-"

"I know. I know. It's normal for a Time Lord. It doesn't make it any less weird. One of my best friends is actually my daughter."

"Which I think is a good thin- you royal pain! Quit being so stubborn!" the Doctor shouted angrily.

"Doctor!" responded an offended and confused Derpy.

"Hm?" the Doctor kept his eyes on his book, "Oh, sorry Derpy. I'm reading A Christmas Carol. Scrooge is such a total grump. This story could use flying sharks. Like I was saying, it's a good thing. She's your best friend and daughter. You outta love her so much, Changlings in Saddle Arabia should feel a disturbance in the force."

"I know, but..."

Derpy paused long enough that Doctor turned the page again.

"She just..." Derpy started again, "She's just so different. She's not the Dinky I know, she has too much Pinkie Pie in her. She's not the Pinkie Pie I know, she's has too much Dinky in her. I just feel like she's a completely different pony."

The Doctor looked up from his book.

"I know. I know," Derpy said before he could speak, "She IS a completely different pony. You know what I mean. It just feels like Dinky is gone and Pinkie Pie is pretending to be her."

The Doctor put his book on the table next to the candle. He got up from his chair and approached Derpy's side of the bed, looking her directly in one of her eyes. His own eyes were warm and caring.

"Derpy," he began, "Her personally just had a bit of a reboot is all. She has the same memories and thoughts as the other Dinky, she's just a more hyper shade of pink. Trust me. Give it a little bit of time and she'll be your little muffin again."

Derpy sighed as she tilted her head downwards and closed her eyes.

"Maybe you're right."

The Doctor kissed Derpy's cheek.

"Get some sleep, Derpy."

The door slammed open and the lights turned on bright. Dinky stood in the doorway looking nervous and worried.

"...or nevermind," the Doctor mumbled under his breath. He turned to Dinky with a raised eyebrow, "What's wrong, Dinky?"

Dinky took a dramatically deep breath and began talking at break neck speeds.

"Well, I was preparing Hearth Warming breakfast and talking to myself to pass the time. When, suddenly, I heard a magically noise from the other room. I went to check it out, and it was Twilight and she said she needed my help. So I was all like, 'What's up, Twi? Having a We-Woke-Up-Way-Too-Early-For-Hearth's-Warming party?' and she was like, 'No, the fate of Ponyville might be in the balance and I need all the help I can get.' Then I ran up here to get you, but you were all like, 'What's wrong, Dinky?' So I had to start explaining."

Dinky stopped talking and started gasping for air. Derpy looked completely lost which wasn't mirrored by the Doctor, he wore a smug smile.

"I knew it!" he said excitedly, "I knew Ponyville didn't look right! I knew I wasn't crazy!"

The look that both Derpy and Dinky gave him caused him to roll his eyes.

"Oh, shut up. Let's just go and see what the fuss it about, shall we?"

Dinky reappeared in the store front with the Doctor and Derpy in tow. Twilight had fixed her mane and seemed to have physically calmed down. Her eyes focused on each of them respectively, getting stuck on Derpy. Her expression went from calm to shocked in less than ten seconds.

"Ditzy!" Twilight said, approaching the mare and analyzing her, "What in Luna's name happened to you?"

Derpy smiled and shook her head.

"Don't worry, Twilight," Derpy assured the Princess, "I'm fine. I'm also not what's important here. Plus I'll explain later."

Derpy looked to the Doctor for confirmation of whether they would explain it later. The Doctor shrugged in a way that said 'Probably.'

"Anyway," Derpy continued, "What's going on?"

Twilight seemed reluctant to leave the issue, but did agree that there were more important problems at hoof. She made a mental note to press Ditzy for answers later...perhaps over tea and muffins.

"Well," began Twilight as she paced about, "Ponies have been disappearing over the last two days. I noticed it in the market when a few venders had refused to show up. I didn't think much of it, as ponies travel for the holidays. Then this morning there were almost no ponies walking around. So I wrote a letter to the Princesses noting this odd phenomenon. As I went to go send it, I noticed Spike was gone and I couldn't find him anywhere. I checked the Carousel Boutique but he wasn't inside. Not only that but Rarity and Sweetie Belle were also missing. I checked the rest of the other Bearers and found all of them to be missing. Even Applejack, who's as rooted to this town as her apple trees. I had almost given up hope when I teleported here and found you, Pinkie."

The Doctor put a hoof to his chin.

"So ponies are disappearing," he said, "Which explains the lack of them when we had first arrived. Any other clues?"

Twilight began looking uncomfortable, eyes tracing the wood grain on the floor.

"I did find one," Twilight said, a sadness saturating her tone, "Before I came here, I checked the Carousel Boutique again and I found something that...scared me."

Twilight visibly shivered at the last bit. Dinky walked over to Twilight and pulled her into a hug.

"Don't you worry your pretty little egghead, Twilight," Dinky said, trying her best to comfort the alicorn, "Dad is totally gonna fix this and we can all have hot chocolate after, okay?"

Twilight pushed out of Dinky's hug to fix her with a confused look.

"Dad?"

Dinky's pupils shrank as she tried to maintain her poker face. A pretty decent poker face for that matter. If she didn't have such a hard time holding playing cards, she'd make quite the living out in Las Pegasus.

Dinky took a few steps back until she was between the Doctor and Derpy. She wrapped a leg behind the Doctor's neck.

"This cool Daddy-O here, Twi," Dinky gestured to the Doctor, "Yo, this cat's so cool...he's radical...ya dig?"

Twilight looked Dinky up and down with a serious expression. She then rolled her eyes with a slight smile.

"Oh, Pinkie Pie, you're so eccentric," Twilight's smile dropped and her whole face seemed more grim, "Anyway, if you'll follow me."

Twilight walked out of the store and into the snow, beginning the short walk to Carousel Boutique.

Derpy chose to fly near Twilight, mimicking the alicorn's silence. The Doctor and Dinky lagged behind them, walking at the same pace.

"Radical?" the Doctor mumbled loud enough for Dinky to hear, "Where did you learn that word?"

"Spoilers," Dinky giggled, "Pinkie learned them for some little bit she did for Rainbow Dash in her past and I'm assuming your future, Daddy. I'm not sure if she even used 'radical' but she sure should have."

The Doctor laughed softly, "I look forward to it, then."

"Doctor!" Derpy called from up ahead.

The Doctor and Dinky galloped around Carousel Boutique to where Derpy and Twilight were standing. In the snow before them stood a stone statue of a small dragon. His mouth open in an eternal scream.

"Wow," said Dinky, "I knew Spike liked Rarity and all but a stone likeness of himself is a bold gift."

"But that's just it," Twilight spoke up, "This isn't Spike's Hearth's Warming gift to Rarity. He made a pair of sapphire earrings for her. Also, the expression. Why would Spike, let alone anypony, make a statue that looks so...terrified?"

"Good point, my dear," the Doctor noted, fishing his Sonic out of his pocket, "Let's see if there's more to this statue."

The Doctor pressed his Sonic a few times looking for a specific frequency.

"What in the world is that, Time Turner?" Twilight asked, her student nature getting the better of her.

"Hmm? Oh this? It's a Sonic Screwdriver. Emits sonic waves to do loads of neat things: analyze stuff, unlock doors, assemble cabinets at ponies. You name it."

"Is it a tool you need often in your clock repairing?"

"Look," the Doctor began to scan the statue, "Since Derpy is a bit of a blabbermouth and is going to explain everything later, I'm gonna tell you right now that I don't repair clocks for a living. Trying to maintain the lie is exhausting and there are more important things to worry about."

Twilight made a slightly confused face at the Doctor, storing this information for her later talk with Derpy. The Doctor looked at the tip of his Screwdriver to confirm his suspicions.

"That statue there isn't a statue. It's Spike, but completely solidified. All of his insides are perfectly preserved but hard as a rock."

"Solid rock?" Twilight brought a hoof up to Spike's face and stroked it, "Do you think it might be the work of a Cockatrice, Time Turner? They have the power to turn things into stone."

"It's the Doctor, Time Turner is a pseudonym. To answer your question, it would make sense if this were just stone but this is something else. It's similar to a material that I'm familiar enough with to know we're in danger. Fortunately it seems to be remotely linked by some kind of arcane force."

"Linked to what?" asked Twilight.

"Let's go find out."

As the snow-covered road gave way to snow-covered snow, the group made their way out of Ponyville and towards the outskirts of the Everfree Forest. The Doctor slowly led the way waving his Sonic Screwdriver in front of him. The Screwdriver emitting various frequencies depending on the direction it pointed. The rest of the group walked a few yards behind the Doctor.

Twilight had a lot of important things on her mind. Each item important in its own right and needed to be dealt with. She shook her head as if to scramble the items on her mental To-Think List, rearranging them based on what she could acomplish more immediately. Reassessing the list, she turned her head to Derpy.

"So, Ditzy," the words stumbled awkwardly out of Twilight's mouth, "Since we have some time to talk. Maybe you could...you know....explain some...stuff."

Twilight punctuated her sentence with an awkward cough. Derpy frowned.

"I suppose," Derpy drug out the last syllable, "Twilight, I'm a time traveler. I-"

"Impossible," Twilight interrupted, falling into full egghead mode, "While time travel isn't completely impossible with the aid of a carefully crafted spell. The fact remains that you are a pegasus, so you would have no access to magic. While non-magic time travel methods have been theorized pretty extensively, even by Starswirl himself, no full scale prototypes have ever been constructed. Even building a 1/16th scale model of a non-magic time machine would require an amount of power equal to roughly three times the magic inside all the unicorns of Equestria combined."

There was a brief moment of silence as Twilight mentally fact-checked herself. Derpy cleared her throat loudly to get the alicorn's attention.

"I'm just a passenger, Twilight. I travel with my husband, the Doctor. He uses his alien space-time ship-machine called the TARDIS. I look different from the last time you've seen me both because I'm from the future, and because I've spent so much time traveling through time that I'm older than I should be."

Twilight stopped dead in her tracks causing Derpy and Dinky to also stop. Her face was an odd mixture of expressions ranging from shocked to confused to worried.

"Wait a minute, let me get this straight," Twilight's eyes were locked on Derpy as she tried desperately to process the information, "You're married to Time Turner, whose real name is the Doctor, a space alien who you've been traveling through time with for Celestia knows how long, and you're also from the close future. Did I miss anything?"

Stands of Twilight's mane sprung out of place until she looked as crazy as when she had teleported into Sugar Cube Corner. Derpy and Dinky were silent, staring at Twilight.

"We also travel through space," a voice behind her said.

Twilight screamed and shot up into the air with a quick flap of her wings. She quickly righted herself and turned toward the direction of the voice.

The Doctor held a hoof over his mouth to try and contain his giggles. Her cleared his throat and addressed the panicked princess.

"Sorry, my dear, didn't mean to hehe spook you. To answer your question before you ask it, no we can not prove it at the current moment. Unless you happen to have a stethoscope for all stethoscope-related emergencies."

Twilight flapped lightly until her hooves touched the ground. Folding her wings and fixing her hair, she faced the Doctor again.

"Stethoscope?" She asked with a raised eyebrow.

"Yes! The type of alien I am, Timelord, are known for having a binary circulatory system."

"Binary circulatory system? Do you mean you have two hearts?"

"Bingo! Two hearts! So if I-"

The Doctor was cut off on account of being wrapped in a lavender field of magic, the same as the one around Twilight's horn.

Derpy's eyes went wide.

"Twilight! What the Tartarus are you doing?!"

"Scanning him to check if he has..."

The field vanished and Twilight stumbled back a few steps. Derpy immediately rushed to the Doctor's side. The Doctor smiled at her to show that he was fine.

"...T-two hearts....Two hearts...he has two hearts."

Twilight looked up at the Doctor.

"You're an alien?"

"I'm an alien."

"That travels through time?"

"And space."

"Wow...can I ask you a few questions about-?"

"Yes, AFTER we save all of Ponyville and Equestria."

Twilight's face took on a look of determination.

"Right."

"Good," the Doctor said as he walked away, "There's a cave right up ahead. Do keep up this time."

The group began moving again, tailing the Doctor. Twilight giggled to herself.

"I can't believe I never knew there was an alien living in Ponyville. I'll have to scan ponies more often to make sure we haven't been completely invaded."

Dinky's smile fell slightly.

The inside of the cave was completely dark. Twilight lit her horn and led the rest of the group deeper underground. The path was linear and seemed to tilt ever so slightly down. Every few minutes, the Doctor would use his Sonic Screwdriver to check how close the source of the arcane force.

"How much longer, Doctor?" Derpy asked, trying her best to keep the exhaustion out of her voice, "My hooves are killing me."

"Not much farther, Derpy," the Doctor replied, scanning again, "Should be just up ahead."

The cave began to become increasingly lit up as they continued walking. The light seemed to be coming from further into the cave. The cave walls and ceiling seemed to close in until it formed a space as big as a doorway. Beyond the doorway, the cave opened into a huge room. The ceiling reached up to 40 feet at it's highest as it curved to meet the walls. In the center of the room stood a pedestal with a glowing green amulet floating on it. Four identical stone alicorns stood around the pedestal facing outwards, their faces in their hooves.

This isn't what caught the group's attention. Around the room stood a myriad of other stone ponies. No one pony looked exactly the same, but they all shared the same theme. They were residents of Ponyville.

Author's Notes:

I didn't want to cut the story here but I seem to have lost the other really long half of this chapter.

Save often, kids.

Regardless, here's this part and I'll try to rewrite the next part into its own chapter.