The group had been traveling space and time for a while now, experiencing every moment of it, even Rarity had a story or two to tell of adventure. However, there next stop would change everything.

"All right gang," the Doctor spoke. "Let's see whats behind door number 1!" He opened the TARDIS door, and low and behold, they were in Equestria, PonyVille to be exact. "What?" the Doctor questioned, he looked at Spike, who was learning to fly the TARDIS, "What?" the Doctor repeated.

"Doc, I'm getting the feeling that you had somewhere else in mind?" Rainbow Dash snickered.
The Doctor went over to the control panel, "Your right Rainbow Dash, we were supposed to visit this lovely little planet where apples grow out of storm clouds, and lightning falls from trees."

"That sounds dangerous," AppleJack turned to him, "And kinda dumb."
"Well, excuse me for running out of monsters to fight," He punched in the coordinates, "And their we go!"

They heard the noise but felt no shake or rattle, instead they saw something very peculiar.
"What?" They all seemed to say in unison.

"Well that's new." the Doctor quipped is. "My TARDIS in my TARDIS!"
Twilight was the first with a question, "Shouldn't you, I don't know, open it?"

"Well somepony's grumpy today," He looked at it, "But yeah."

As he approached it, the TARDIS within itself opened, while the current TARDIS buzzed a paradox alarm. The Doctor was completely within the TARDIS, "Hello," he called out.

"Hello, Doctor." A message appeared on the TARDIS master screen, "If your wondering why I've sent myself this message its because the worst possible thing has happened..."

"Whats taking so long," Spike said, but as soon as he did the Doctor emerged.
"Everypony out, get out mares and baby dragons first hop to." The Doctor started shouting, "That a girl, let's go."

As soon as they were all out he closed the door and locked it, They heard a very loud noise which shook the whole town.
"There we go crisis averted," the Doctor smiled, "Tea anypony?"

"What was that dreadful noise?" Rarity said, still slightly shaking.
"Not much just a universe exploding within another universe." he said casually.

The others looked at him with a confused stare while he just trotted along, "Well come on then, I have a lot of work to do!" The colt told them.

"Here, in PonyVille?" Rainbow asked, "In OUR time period?" she couldn't quite understand it, they had gone on grand adventures but here they where in a boring part of time.

"Rainbow," the Doctor began. "I have a feeling that this is the most important place in the universe right now." He didn't know how right he was, as they spoke something terrible was happening.

Canterlot Castle
Princess Celestia had achieved something amazing, she had opened what appeared to be a void in time, a way of traveling through it. She could go back and save the alicorns, or stop her sister from turning evil in the first place. She stared into it feeling as though she could see everything at once, but it felt wrong. She turned away, fearing the power that had just been opened. She feared it so much that she locked it away, where nopony could find it, unless they were as smart as powerful as her that is.

PonyVille
The Doctor pulled Twilight aside, "Twilight, have there any been records of ponies that could travel in time?"

Twilight pondered this, not being an expert on the subject, "Not that I know of, but to be honest the only ponies who would know for sure are the princesses. They've been around longer than anypony else!" she laughed at herself, she had never thought of her mentor as being old before.

"Well is there anyway I could talk to them?" He asked with a serious tone in his voice, Twilight could clearly see the concern in his eyes.

"Of course," the unicorn said. "I'll send them a letter right away, asking for an audience." She pulled a quill and paper from her desk and began writing.

Dear Princess Celestia,
I would like to ask for an audience with you, my friend, the Doctor, has been very concerned about something. I wish i could tell you all the details but there are somethings that should be said in person.

Your faithful student,

Twilight Sparkle
Spike sent the letter, it was a matter of minutes before they had a response.

My dearest student Twilight,
I would be happy to assist you and your friend, please come to Canterlot as soon as possible.

"Excellent," the Doctor said. "I'm sure we will get along just fine!" he said in an enthusiastic voice.

As the two friends boarded the train, Twilight was telling the Doctor about proper etiquette when meeting with royalty.
"Yes Twilight, I've met royalty before, you know." the Doctor said, "By the way, what makes you so sure your princess will know every bit of Equestrian history?"

"Because she was there, I mean she is over a thousand years old," Twilight said in a matter of fact way.
"What, oh no Twilight this is a whole new ballgame now," the Doctor said, obviously panicking, "I have to show respect now, I've never met someone older than me, but she's at least eighty years older." The Doctor was pondering something, "Twilight , has she ever, um changed? Like appearance?" He asked in sort of a hopeful way.

"No, she's always looked exactly the same," Twilight said smiling, unaware to the Doctors concern.

The two continued the train ride in silence, not an awkward one more like a 'I'm going to read a magazine but that doesn't mean i don't wan't to talk' sort of way. when the train slowed to a stop, they found that the princess was waiting for them, it was quite a surprise. A royal welcome and all that.

"Hello you two, It's, ah quite nice to meet you Doctor," the Doctor looked up from his bow.
"Princess," the Doctor began, "Have you gotten shorter, younger, and changed the color of your, well entire being?"

Twilight elbowed him in the kidney, "Doctor, this is Princess Luna, Celestia's sister." she said in a 'Duh' sort of tone.

"Oh, yes of course how silly of me," He said, "The pleasure is mine, your highness."
The Princess giggled to herself, "Please call me Luna, I'm not much for formalities." she had said.

They walked to the castle, The Doctor and Luna discussing the stars, making Twilight feel left out.
"Oh and that Super Nova? Brilliant!" the Colt said to the goddess of the night.

"Why thank you," she replied, "Have you ever stood on a comet before?"
"Is that an invitation," the Doctor smiled, "Oh I absolutely adore your work, but I do have one question for you. Ever heard of Gallifrey?"

The Princess stopped, "Yes I know of it, their people almost wiped out the whole galaxy, but something stopped them."
The Doctor smiled, "Your welcome," he said in a very calm sort of way.
The Princess gasped, "Your THE Doctor?" she asked. "I'm a huge fan of yours, you've done so much good for my sky."
"Well," he tried to sound modest but abandoned the idea half way through, "Yeah, I mean how could i let anything so lovley go to waste.?" he asked in a cocky tone.

"How old are you now?" the princess asked, "Word on the stars was that you where about 900."
"920," he said in a 'Close enough' tone.

Twilight began to gag, she was sick of there talking about subjects she had no clue about. She was happy when they finally arrived. "Okay, here we are, thank you for escorting us, Luna." the Unicorn announced.
"But Twilight, I want to keep talking to Luna, she's quite interesting!" the Doctor tried to explain, but ended up sounding like a foal. Twilight took this advantage.

"Well, maybe we can set up a play-date for you, but for now isn't there something you just had to ask Celestia?" She said, the insult portion of it had made Luna laugh.

"Ugh, fine." the Doctor finally gave in. "But can we hurry this up? It is a matter of life or death."
Luna did a little fan-girl squeal, "You on one of your adventures right now? What is it? Can I help?"

The Doctor looked at Twilight in a sort of 'I know my way with the fillies' sort of cockiness, "I'm sorry but like Twilight said it is dangerous, But perhaps 'Mum' over hear," he motioned at Twilight, "Will let us hang out later."

The two departed Luna, much to the Doctor's displeasure, "I think your jealous that I'm famous to a princess, where as your the student of one," he said almost as boastfully as Rainbow Dash, "I'm just kidding, but you better set up that play-date!" he said in a humorous voice.
When they approached the throne room the doors opened, it was very tall and regal. At the end of the pathway was sitting the ruler of Equestria. "Oh, hello Twilight! Hello Doctor, so good to see you again." The Princess said elegantly.

"Greetings your Majesty," Twilight bowed, The Doctor however felt that something was wrong.
"You, y-your why I'm here." He said, confused by what he felt, ancient but young, so close yet so far off. The Doctor spoke on an angry tone, "You, are why my TARDIS brought me here, you've created something." He started looking behind all of the curtains. Twilight was infuriated.

"Stop embarrassing me!" she shouted at the Time Lord. But he turned around and shouted back.
"Your teacher is why the TARDIS is dead!" He was furious. But he was interrupted by Celestia.

"Doctor, what do you know? Who told you these things." She demanded. The Doctor turned around determined to strike fear in her heart.

"Did you not see me?" He asked, "When you stared into the Time Vortex, a being of unimaginable power, bathed in the blood of a billion galaxies, the oncoming storm, the scourge of Gallifrey?" He finished in success.

"No, your not real, they said you were dead!" Celestia said, "How do you know about me looking into the Time Vortex?
The Doctor just smiled, "I didn't, you just told me." Celestia sighed and looked at her student.

"He's correct Twilight, I looked into something that should never be seen, I opened the powers of the lords of time." The princess looked down and they all began to talk.

Secret passage
Luna loved to walk in the secret places of the castle. It was like a mini adventure, just for her. She had found every nook and cranny that the castle had to offer, secret passages, hidden rooms, and most importantly a door that only she could open. It was a door that only an alicorn could pass through. As she entered her secret place however, she saw something that hadn't been there before some sort of arch-way. She decided that the best thing to do was use her magic on it, It started to make a very strange noise, it produced a bright light that began to spin as if it were a hurricane. She looked into it, she suddenly felt something. Knowledge, more than she could bear. Power, greater than Nightmare Moon's. Fear, the fear of all possibilities. The Princess of the Night felt amazing, she decide that she wanted everyone to see her like this and began her march to the throne room.

Throne Room

"Look if you just tell me where it is I can fix all of this" the Doctor begged to Celestia.
"Absolutely not! I can use it to protect my subjects from any danger." The stubborn Princess declared.

"YOUR not even supposed to have it! By having it you've created a paradox, your people will die if I can't fix it soon!" He yelled.

"SHUT UP!" Twilight said, "Doctor explain what my teacher did wrong, Okay?" She pleaded.
"Yes, it must all be very confusing," he admitted. "Your teacher opened the Time Vortex, no creature but the Time Lords are meant to look into it. The Universe is collapsing through it because it's unstable, It was meant to be opened with Time Lord science not alicorn magic. If I don't close it, the TARDIS will die, and so will all of you." He finished with a sigh.

"All of us will die?" Celestia said, being the wise pony she was she noticed his choice of wording, "But you won't?"
He looked up, "Please just let me help!" he begged, "I don't want to watch you all die!"

Their conversation was interrupted by none other than Luna, who had a strange smile on her face. The group looked up but only the Doctor spoke.

"You've killed us all," he looked up at Celestia, "Now I have to save you, stand aside!" He walked over to Luna, "Luna, it's the Doctor, can you tell me what you see?" He asked, Luna responded in a voice that was not her own.

"I see what was and what will be," The voice grew louder, "I see the shattering of Gallefrey, and your precious blue box! I see what you fear Doctor!" She used her magic to lift him, and hurl him into a marble pillar, the pillar itself lost a chunk.

Twilight ran over to him, "Doctor! Please tell me your okay!" She shouted at him, nothing. She put her head to his muzzle, no breath.

"I'm sorry Twilight," Celestia said, "But we must leave now, my sister is not herself!" The alicorn princess lifted her pupil with magic, and flew past her sister out the door. Twilight's tears wouldn't allow her to see where they were headed. She trusted that Celestia would have a plan to defeat her possessed sister.

PonyVille
Rainbow Dash was at home, relaxing with a nap. It was the most peaceful sleep she had gotten in a while, considering she wasn't flying through a Time Vortex while she slept. Her comfort however came crashing down when she received a knock on her door. She grudgingly got up and went to answer it, Fluttershy was at the door. "Hey Fluttershy," Rainbow yawned, "What's up."

For the first time in her life Fluttershy spoke with a very serious tone, "The princess just carried Twilight into town, something terrible has happened." The two friends flew towards the library, Twilight sat next to the princess. Rainbow Dash saw that she was crying.

"What's wrong?" She asked bluntly, "Where's the Doctor?" Rainbow Dash wasn't worried, the Doctor could take care of himself.

"He's dead!" Twilight shrieked, "He's dead and now we're all doomed!" She gasped for air. But Rainbow Dash just snickered, slowly it turned into laughter.

"Oh, Twi," Rainbow took a breath, "You had me goin' there, seriously though were is he?" She found her response in a slap from Twilight.

"You're a terrible pony!" Twilight yelled, "How could think I'm lying about somepony's death!" Rainbow was pissed at her friend for slapping her, but then she remembered something.

"He didn't tell you?" The cyan mare asked, Looking around at their other friends who had joined them. "He only told me? What a stupid colt," she sighed. She looked at Twilight, "He's fine! He can't die, he just changes." Rainbow Dash said in a laid back tone. "He'll be fine in a jiff." And as if she could see into the future they heard somepony speak.

"Right you are Rainbow Dash!" The new Doctor said. He turned for them, "New body, nice isn't it? I feel like I know what I'm doing now!" The other ponies just stared at him, he was different alright. Light grey fur, a black mane(combed into a funny fashion), same cutie mark. "Now, on to business." he said, "Can I have something to eat?" The others just kept staring.

"Who are you?" Twilight asked.
"Twilight," He looked at her, "I'm the Doctor. The soul survivor of Gallefrey, the on-coming storm. And apparently I'm a gloater, nasty habit to fix." Twilight wasn't sure if he was talking to her or himself at this point. "Now can I get something to eat?"

Next Chapter: I'm alone part 2 Estimated time remaining: 26 Minutes