Doctor Whooves and the end of harmony

by Ruby Lightning

Rating: teen
Tags: Romance, Adventure, Crossover
Length: 1838

The doctor and his friends travel through time and space. Will Ruby Lightning be able to control him before he goes too far?

After a strange message from Discord, Twilight and a strange stallion named Ruby Lightning find an amazing blue box and chestnut pony in the depths of the Everfree forest. Follow the Doctor and his companions as they travel through time and space to unravel the secrets of Equestria and beyond

Published 1970-01-01 00:00:00 UTC
Last updated 2015-02-23 00:20:02 UTC

The Arrival

It had been two days since Discord made his statement and Twilight was still trying to figure it out.

“Twilight will you please explain to me what exactly is going on?” Spike asked as Twilight ran around checking readings on some machines that Spike didn't recognize.

“Ever since Discord had those, “complications,” we've been getting readings that are off the charts!” Twilight responded.

“Readings of what!? And from where?” Spike asks, knocking over a book while he jumps.

“I don’t know what they are, but they’re coming from the Everfree Forest.” As Twilight asks this, a new pony knocks on the door, and Twilight opens it to reveal a dark blue unicorn with a long deep red mane and tail, along with glasses a slightly darker shade than his coat.

“Oh hi, I’m a new pony in town, and I was wondering who was in charge of the town, and, seeing as there was a castle, I thought I would start here.” The pony said.

“Oh, I’m not in charge, that’s Mayor Mare that you’re looking for Mr. . .?”

“Oh, my name is Ruby Lightning, but you can call me Ruby.” The colt said, laughing.

“Okay, Ruby. Ummmm, you’d better get inside, I see Pinkie Pie coming.” Twilight said as Ruby turned around and his ears dropped.

“I thought I got away from her!” He exclaimed as he rushed inside and closed the door behind him. “How did she figure out my hologram so- wow. This place is amazing.” He said as he walked further in.

“Do you like it?” Twilight asked, watching Ruby admire the castle. “I only recently came to living here, I used to live in the library in the town, but there was a problem.” She said, looking away.

Oh, I've heard about that problem with Tirek, to be honest it’s one of the reasons I came here.” The unicorn said. "I make reports for a Manehatten newspaper called The New Colt Times, and I was hoping I could make a report about the events that happened.” Ruby said shyly. Twilight looked at him strangely and then smiled.

“Well it’s not like this is the first reporter that’s come for the story, but honestly, whatever you've heard is all there is to tell. I fought him off with the help of my friends. That’s all.” Twilight smiled. “Now I think Pinkie’s gone, you should probably go talk to the Mayor.” She said pushing him out of the door. After she closed the door behind him, she sighed. “He actually seemed like somepony who would treat me like a normal mare.”

      “Soooo, who was that guy?!” Said a voice behind Twilight.

“Gah!” Twilight exclaimed. “Pinkie, how did you get in here?”

Pinkie held up a key, “We all have keys, remember?” Twilight sighed and began walking away. “Hey!” Pinkie exclaimed, bounding after Twilight, “You never answered my question, who was he?”

“He was some reporter that just wanted to talk to me so that he could get famous for meeting me.” She said, trying to look OK. “It’s fine though, I’m kind of used to it.”

“Okey-dokey-lokey!” Pinkie said happily. “I’m going to go throw him a party!” She began bouncing away to Ponyville. Twilight sighed and began to walk back to the main castle throne room to look at the map of Equestria when she heard the sound of a large object crashing in the Everfree forest.

“What in Celestia’s name was that?!” She yelled. “Spike! Keep things in order while I go check out what that was! I’ll be back soon.” She went running out the door and towards the forest. She saw smoke coming out of the trees and tried to make out what it was through the trees. As she neared it, Twilight realized that it was some kind of blue box with words on top. “What the Tartarus is a police public call box?” She asked to no one in particular. “Oh! There’s somepony by it!” She rushed over and saw a chestnut pony with dark hair lying next to the strange box. He was obviously a stallion and had a cutie mark of an hourglass on his flank. “Who the heck are you?” Twilight asked and he began to stir. “Time to get some answers.”

The Doctor

“Hello?” Twilight asked the pony, who had just woken up. “Who are you, and what is this box-thing?” The chestnut earth pony looked at her strangely and then his eyes widened and he quickly look down at his hooves.

“Oh my God!” he said (Twilight noticed a strange accent in his voice) “I’m a horse! How did this happen?”

“Uh, actually we’re all ponies, and WHO ARE YOU!” Twilight yelled at the stranger.

“Oh, my apologies, I just didn't think any of this would happen when I was trying to close up rifts between other dimensions! This is so strange, that I would become a, a, pony!” He looked around and saw Twilight glaring at him. “Oh, sorry again, I’m the Doctor.” He finally said.

“Doctor who?” Twilight asked. The strange colt was running around looking at all the different trees and creatures running around.

“Nope, just the Doctor, thanks.” He said. “Will you look at this! And you! You are a beauty. An Alicorn!” He said, examining Twilight, walking around her. “What is this mark?” He said, looking at the stars on Twilight’s flank.

“Um?” Twilight said, blushing, “That’s my cutie mark, everypony has one.”

“A cutie-whatzit?” The Doctor asked. “Oh. OH! That’s hilarious! What does it do?”

“It explains your special talent, um, Doctor? What is going on here?” Twilight asked. The Doctor was about to answer, probably with something else that made no sense when they heard a voice coming their way.

“Princess Twilight, are you in here? I wanted to apologize for what happened earlier!” Twilight groaned as she realized it was the unicorn from earlier. “Princess? Princ- oh my Celestia!” He said as he walked into the clearing. “What is going on here?!” He said, his eyes wide, backing up into a tree.

“Another unicorn!” The Doctor said, walking up to Ruby. “How do you exist?!”

“What is this box?!” Ruby yelled, beginning to regain his composure. “And Princess, who is this?” Twilight looked between the Doctor, who was looking at her with an amazed look, and Ruby Lightning, who seemed like a confused child. She sighed and began walking away.

“Twilight, wait!” She heard Ruby yell behind her. “What is going on?”

“How should I know?!” Twilight yelled, turning towards Ruby. “I’m just as confused as you are!” She ran away, back towards Ponyville. Ruby slowly walked back towards the clearing.

“Well, hearing that, I’d say that you two are a couple?” Asked the Doctor, who was leaning against the blue box.

“Are you joking?” Ruby asked, still wary of the strange pony with the box. “I only met her just this morning! I only wanted to talk about what happened with Tirek.” Ruby looked down with a depressed look on his face.

“You know, I might be able to help with that.” The Doctor said. “But first, I need to figure out why the TARDIS brought me here.” He opened the door and went inside the blue box.

“How do you fit inside that box?” Ruby called, and walked over to the strange box. “Doctor, what are you- I say it for the second time today, wow! This box is bigger on the outside!” He looked around as the Doctor stopped rushing around the room inside the box.

“Is it?” He said sarcastically, “I've never noticed!” He resumed running around pulling levers and flicking switches. “Argh!” He yelled all of a sudden, “these stupid hooves are too big to use my TARDIS!” The Doctor looked at a screen and his eyes widened. “Oh, oh no, no, no, no, no!” He rushed out of the box, leaving Ruby still confused.

“Doctor!” He yelled, “Please come back, tell me what’s going on!” When the Doctor didn't return, Ruby looked at the screen and saw coordinates. “This is going to hurt.” His face screwed up and his horn began to spark. A glowing purple sphere surrounded him, and with a pop he found himself at the coordinates. The Doctor was running up when Ruby’s vision cleared, and Ruby began swaying and stumbling around. “Doctor!” I teleported here! You know, I don’t feel too good.” He said before promptly fainting.

The message

As the sun rose over ponyville, Twilight Sparkle was woken by Spike, Twilight’s baby dragon friend, crashing in the kitchen.

“Spiiike!” She yelled. “Ugh, not again.” She said tiredly. She got up out of bed, re-made the bed with her magic, and began walking downstairs. When she got to the kitchen, she saw a mess of pots and pans on the floor, and Spike was underneath a particularly large one. “Spike! What happened?” she asked.

“I don’t know!” He replied. “I was fixing breakfast and all of a sudden the pots and pans flew off the shelves!”

“How could that even happen?” Twilight asked. Just as she said this, a glass jar levitated off the shelf and landed next to her.

“Eeii!” Twilight shrieked and jumped to the side. “OK, what is going on here?” Twilight asks as she and Spike walk outside to see a situation of chaos unfurling. There were ponies floating into the air and random things flying around the place. Twilight and Spike were looking around when they heard a yell and everything fell back to the earth. “You know, I think I know who is responsible for this.”

The pony and the dragon followed the sounds of the yells, Twilight protecting herself and Spike from the chaos around them. They eventually reached their destination and Twilight knocked on the door of a little cottage on the edge of ponyville.

“Fluttershy!” she yelled while knocking, “Please open up!” She heard footsteps approaching the door and, to her surprise, Discord the draconequus answered the door.

“Oh, hello Princess Twilight. Come on in.” He spoke in a stuffed up voice. He walked in with Twilight and Spike right behind.

“Who is it, dear?” Fluttershy said from inside the house.

“It’s me and Spike, we came thinking you would know what’s going on outside, I mean, you are married to the lord of chaos.”  Said Twilight, walking towards her friend.

“Oh! Hello Twilight, it’s good to see you. It’s been awhile since I've seen you.” Fluttershy responded with a hug.

“I know Flutters, but what is going on?” Twilight asked, almost afraid to hear the answer. But, just as Fluttershy was about to say, Discord let out a vicious howl and his eyes glowed. Twilight used her magic to protect the two ponies and Spike, but the house was not so lucky. Things fell off the shelves, and she could hear ponies screaming in the distance. When the chaos died down, Discord turned to Twilight and said,

“Something horrible is coming.”