The Doctor ran around the console, flipping switches and punching buttons

Rainbowdash watched, wanting to know how the ship was able to travel through time

Clock Crasher laughed, "Barely anyone knows how to fly one of these things."

"How does this thing even travel?" Rainbowdash asked, "It's a box!"

"It just looks like a box" the Doctor corrected, "It's a time machine that looks like a box."

Rainbowdash opened her mouth to ask another question but the Doctor interrupted

"And we're here, we should be on the planet of Raxacoricillia" The Doctor said, "The sky has automated clouds."

"Automated clouds?" Rainbowdash asked, "How is that possible?"

"The sky generates them itself, cleans out the nasty weather and such" Clock Crasher pitched in

The Doctor opened the doors, but was surprised by what he saw

"What are we doing here?"

Rainbowdash poked her head out of the box, "We're in Cloudsdale"

"Seems so" Clock Crasher said, "Let's go take a look at the weather facility while we're here."

Rainbowdash rolled her eyes, "Automated clouds you promised me."

The Doctor straightened his tie, "Why did we land here?"

"Let's take a look around" Clock Crasher stepped out towards the clouds

Rainbowdash tried to stop him, but the earth pony was able to step on the clouds easily

"Only pegasi can walk on clouds" Rainbowdash said, "You didn't even have the spell."

"Let's just get to the weather facility" the Doctor said, "It'd be a nice little trip."

The Doctor followed the rainbow Pegasus's instructions to the facility

When the Doctor arrived there were several lab coats were hanging up, the Doctor picked one up and felt his pulse quicken

It was his measurements, there was even a nametag with his picture on it. He was expected

The Doctor took off his current coat and put on the lab coat, making sure to keep the sonic screwdriver with him

Clock Crasher and Rainbowdash put on their lab coats, and put on their own nametags as well

It was a nice little visit, the clouds being mixed and the rain being poured, even the rainbows being mixed

"Where do the colors come from?" Clock Crasher asked

"Good question" the Doctor said, "We're able to see where it gets mixed, but where do the colors come from? It's not as if they come from nowhere."

Rainbowdash shrugged

"Let's look around, see if there's a place we missed." Clock Crasher said

It wasn't long before they came across a giant pair of foreboding iron doors, barring passage to all that approached

The Doctor saw a little scanner, he put up his nametag to it

The doors opened, the musty smell heightening the Doctor's worry about what was going on in there

"Well" the Doctor said, "Allonsironimogi."

The three entered, the doors closing behind them

The Doctor was shocked by the technology of this place, it was more than he'd previously seen in Equestria, he was so awed that he didn't see Clock Crasher wander off

"This technology is way beyond what I've seen" the Doctor said, "I don't like this"

Rainbowdash looked at him, "I think I see a lift."

The Doctor and Rainbowdash stepped onto the metal lift, it began to rise and the Doctor's heart began to pump faster

Then he did a double take, he put a hand to his chest

*Bump bump, bump bump*

'I only have one heart?' the Doctor thought to himself

"Doctor" Rainbowdash said, but her voice sounded off somehow

The Doctor turned to Rainbowdash on his right, but she looked terrified

He turned around, and saw a second Rainbowdash with color on her lab coat

"Good for you to finally come" she said

"Alright, alternate" the Doctor said, "So I was expected, the walkable clouds, the lab coat and name tag?"

"All my personal work" Rainbowdash said

"Then what do I call you?" Rainbowdash challenged

(God this going to get really confusing really quickly)

"I don't know what you want, but-"

"I'll show you, oh gracious Doctor" the scientist said

She gestured with a hoof to a small foal

Her coat was orange, spattered with bruised and blood. Her mane was matted and barely held its original color of purple

Rainbowdash gasped, it was Scootaloo

"I'm sure you've been wondering where our spectra comes from" the Scientist continued, "We take the foals that fail their flight tests, and well, do this."

Scootaloo was dropped into a pit, there was a sound of grinding that wasn't able to drown out the screaming, then bright orange and purple spectra was pumped out

"Th-that's sick!" Rainbowdash spat, "How could you even do that!"

"Sedate them" the Scientist ordered

The Doctor didn't even have time to react before getting walloped upside the head with a heavy object

[…]

The Doctor shook himself awake, he was strapped down to a table, Rainbowdash was on a similar table across from the timelord

"So you decided to wake up" the doppelganger said

"You know, I'm going to stop you." The Doctor said, "You get one warning, and this is it."

"Says the man who's strapped down on a table" Rainbow scoffed

The Doctor breathed deeply, now it was up to Clock Crasher

[…]

Clock Crasher had watched the proceedings from a distance, he knew what he'd likely have to do

He went from machine to machine, hitting some switches and unscrewing several important pieces

Now it was time to hit it

He was sneaking across the factory floor before he heard a voice from behind him

"Well lookie who we have here, a spy?" it was over the intercom

A robotic arm reached for the earth pony but Clock Crasher dodged it and bucked in order for it to have trouble getting a hold on him

The version of Rainbowdash in charge of the factory then had a bold idea, she challenged him to meet her by the Pit

Clock Crasher complied, but with a cunning plan of his own

"Oh no…" the Doctor realized what it was

"Doctor!" Clock Crasher called, "Take care of her alright?"

"You can't!" the Doctor protested, "What will I do without you with me?"

"This must be done" Clock Crasher looked at Rainbowdash

He jumped on her back, preventing her from flying. They both fell into the Pit

"NOOOOOOOOOOO!" the Doctor cried out

Rainbowdash was in mute horror, the machine gave its best rainbow of colors yet

The bonds holding the two gave way, the Doctor looked down into the Pit

"They're gone" he said, "There's nothing we can do now."

"She deserved it" Rainbowdash spat

"Did she?" the Doctor questioned

"…No…" Rainbowdash choked back a sob, "Oh Celestia!"

"Come on, let's get back to the TARDIS." The Doctor nudged her

"Alright" Rainbowdash said

[…]

The Doctor ran into the console room, putting away the lab coat as a memento to Clock Crasher

"Where to next?" the Doctor asked halfheartedly

"Can you take me home?" Rainbowdash asked

"Are you sure?" the Doctor asked in surprise

Rainbowdash nodded, "This isn't what I thought it would be, I never knew ponies would die."

"I wish it wasn't as common as it is" the Doctor muttered, "Right! Let's get you home once again."

[…]

Rainbowdash stepped on the soft clouds of her house, she waved goodbye to the Doctor

The timelord turned and stepped back into the TARDIS

"So where do I want to go now?" the Doctor asked himself

*Ring Ring*

The Doctor looked over and saw his phone ringing