Chapter 2

Starlight ignored the question and grabbed Twilight's mane with her magic

"We don't have time for this!"

The Doctor nodded, "The sooner we stop what's going on the sooner we can grieve."

"Don't act like you're part of this!" Starlight snapped, "We all could do just fine without you!"

The Doctor rolled his eyes, he forgot how stubborn she could be when she was angry

"We don't have time to blame me for anything" the Doctor asserted, "We can take your poorly hidden secret passage."

Twilight had gained her senses and was working on moving the wooden pallet in the way of the ventilation systems

"Right then, Adelante!" the Doctor grinned

The Doctor was pushed into the large vent first, as Starlight wanted him where she could see him

The Doctor was sure that there was something he missed, something important but being recently regenerated he still wasn't working properly, and likely missed the important clues

He pushed out a grate out of the way and came out nearby the stinking sludge river

"What's in that thing?" the Doctor asked as he got out of the way

"That's where they get the things they put in the gas, and where they put the ones who died because of it." Twilight stretched her wing

"For a Pegasus you don't use your wings much" Starlight observed as she put the grate back

"Brand new me, haven't gotten the hang of anything yet." The Doctor waved it off, "But I think that the castle should be our next stop."

He knew where he was now, he thought he was on another planet but something was wrong

The Empire was still in Equestria

[…]

The queen was looking at her kingdom with her daily smirk of triumph, it had been easy to usurp the throne and take the kingdom for herself

The not so easy part was getting the machinery, luckily for her the Equestrians had already supplied her with the hard parts

One of her loyal subjects had entered her throne room, "My queen, the dragon was exposed."

"One with his mindset it was bound to happen sometime soon" the queen responded, waving a hoof

"But he told us that they found somepony else" the little holed hoof creature persisted, "And this one's clever, even more so he's a nonentity!"

"Another one?" now the queen was interested, "That makes three in the last week."

"What do we do?" the creature asked, smirking in anticipation

"Don't let those stolen emotions control you" the queen scolded, "As for our plan, we do the usual."

[…]

The Doctor led the charge, but his destination wasn't the castle, it was something parked a few blocks away from it

Unfortunately they were spotted by a few hazmat ponies, and they were being chased through the streets

"Where are we going exactly?" Twilight panted

"You better not be leading us into a trap!" Starlight growled

"Just shut up and run!" the Doctor said irritated

It was one thing to run into a former companion, it was another that they were going to use every opportunity to take pot-shots at you

The TARDIS was in view, and the Doctor subconsciously began to run faster, throwing open the doors

"Get inside!" the Doctor shouted, "We'll be safe in here!"

"Are you kidding?" Starlight stopped in front of the timelord, "There's no way that thing will protect us!"

"Just for you" the Doctor rolled his eyes, "Shut up, and before you ask, shut up! Now get inside!"

Twilight wasn't looking where she was going, and knocked the other two inside the TARDIS, and the Doctor closed the doors behind them

"Whoa…" Starlight was awed

During the trip the Doctor took the time to improve the TARDIS design, there were four floating pillars on the outside of the hexagon of metal grating, the whole console room was a decagon while the light blue lighting were shaped like octagons

The time rotor was a cylinder like before, but the inside it held several upright crystals that moved up and down whenever the TARDIS began to travel, as for the controls they were on a hexagon much like the metal grating, including the old computer screen and keyboard and the random buttons and switches, the handbrake was that of an old fashioned car

The Doctor ran up to the controls, now friendlier to his hooves, and began to press buttons

"What… It's bigger…" Twilight was in shock, "But how… This isn't possible!"

"It's bigger on the inside!" the Doctor smiled, "Welcome to the TARDIS, that's Time And Relative Dimension In Space."

"I'm not impressed" Starlight simply said

"Of course you're not" the Doctor said, "After all, you've seen this sort of machine before."

"What are you saying?" Starlight raised an eyebrow

"Being newly regenerated I had missed it, but the TARDIS helps me along" the Doctor explained, "And you were a companion to the Doctor and Ditzy Doo, or Derpy Hooves."

The Doctor went on, "I had missed this piece of information, but only someone who had been with the Doctor and been abandoned would act as critical and suspicious as you've been."

"You're as clever as he warned me" Starlight smiled slightly, "Okay you're right."

"Starlight what's he mean?" Twilight asked

"I was a companion to a time travelling alien" Starlight said simply

"Well that's underselling it" the Doctor said

Twilight shook her head, "This has to be some kind of prank."

The TARDIS shook, it seemed that the hazmat ponies were ramming the sides

"I thought you said it'd be safe in here!" Starlight shouted

"Nothing can break through those doors" the Doctor said calmly, "But that doesn't mean they can't pick it up."

"So they're moving the TARDIS, but where?" Starlight asked

"Who took over Equestria?" the Doctor asked

"Queen Chrysalis" Twilight answered, "She's who we planned to stop."

"Ever met her face to face after her takeover?" the Doctor persisted

"No" Twilight looked at him like he was crazy, "She'd capture me like she did my friends."

"Well prepare to meet her" Starlight said, "They're likely taking us straight to her."

The Doctor knew now what he had to do, all of the beauty of Equestria would never happen if the queen won, it was his job to stop her

'And to think I was going to escape into space…' the Doctor thought

[…]

Queen Chrysalis looked at the blue box brought before her, judging it

"Have you tried to door?" she asked

"No magic could get it open" her changeling explained, "Nor brute force."

"Watch and learn" Chrysalis began to use her magic on the door

*click*

"You see?" Chrysalis felt a surge of stolen pride, "It was simple to-"

The door opened, and out stepped a few ponies

"You didn't unlock that door" the Pegasus stallion said, "And you won't be able to, ever."

"Now this is interesting" Chrysalis said, "What is your name?"

"I'm the Doctor" the Doctor answered, "And it's interesting, what you've done with this place."

"I simply took it, the machines were from years ago." Chrysalis said, "Doctor, you seem… off."

"I don't suppose that you've captured a stallion named Time Turner have you?" the Doctor changed the subject

"He was not a match once he was cornered" the queen smiled, "What is your worth I wonder."

A changeling scanned the Doctor

"He is no one"

"The clever nonentity" Chrysalis felt adrenaline, "What is your species name?"

"He is nothing"

"You don't have my species in the databanks" the Doctor smirked, "Interesting"

The Doctor hadn't noticed a group of changelings gathering some sort of goop, until it was flung and splattered all over the hooves of our trio

The Doctor remained uninterested

"You know something else I noticed when I got my gears turning?" he asked Starlight

"What?"

"It's that Spike would never in his right mind have worked for the queen" the Doctor explained, "And I seem to remember that Chrysalis here has the ability to control minds."

"You mean…" it dawned on Twilight, "He wasn't a traitor?"

"Not at all, he was simply under the influence of a big bug." The Doctor said, "I should have noticed but you know why I didn't."

"And now you are here, powerless."

"Not me, never!" the Doctor frowned

"I can taste your emotions from here" Chrysalis continued, "Such rage, pain and anger, it is so delicious!"

"Mind you I quite like hope" the Doctor turned to the window, "And I can see it coming now."

Several ponies crashed through all of the windows, all of differing shapes sizes and kinds, there were pegasi and earth ponies and unicorns, all of them wearing basic weaponry

The Doctor was able to name a few he recognized, there was Big Macintosh, Scootaloo and Colgate

"Changelings!" Colgate shouted as they raised their weapons

"Your plan was to rush my castle?" Chrysalis laughed, "I can easily over power all of you!"

"You know one of the interesting things about your ability to steal emotions" the Doctor continued, "Is that the bodies of ponies resist it, thus allowing you to drain them."

"I hope you're going somewhere with this one" Starlight said, "I hate it when you stall these things!"

"But what happens if a pony were to allow you to steal their emotions?" the Doctor asked, "It was be as if someone were overloading a circuit!"

"And we just so happen to have a creature with quite a bit of emotion" Scootaloo looked at the Doctor

The Doctor shook off the goop, and began to slowly walk up to the queen

"Because I know why I'm not on your list of species" he said, "I can tell you exactly what I am."

"Is it important?"

"Oh yes" the Doctor said, "Because with all your stolen emotions one that you have is fear, fear of the timelords."

Chrysalis reared backward, "They all died years ago!"

But she could feel it from the Doctor, emotions of guilt and pure cold fury, the fury of a timelord

"And yet you know I'm exactly what I claim to be" the Doctor said, "Let's make a deal, I find you and your children a new home, and you never return to Equestria."

"And if I refuse?"

"Then I'd have to stop you." The Doctor sighed, "Why does nobody ever just take the offer?"

It was then that all of the ponies in the room let out what they were feeling, opening their hearts and letting it all out

It was too much for most of the changelings, as they passed out and hit the floor, convulsing

Queen Chrysalis was fighting the immense pain in her head, she didn't want to give up but she had her children to think about, her loyal subjects

She had to protect them, at any cost, but if that cost was her own pride? This was her revenge!

"Alright, alright!" Chrysalis shouted, "I take your offer!"

It was then that the pain stopped, and she stumbled to check on her changelings

"Why was it that easy?" Twilight asked

"The changelings are her kids" the Doctor said, "Would you sacrifice your pride in order to save yours?"

"What will you do with my species?" Chrysalis asked

"Do as I promised" the Doctor said, "Take you to a new planet and let your race live on, until time does what it does."

"You mean you aren't going to execute them?" Colgate asked

"Why would I?" the Doctor frowned, "They gave up, no need to kick them while they're down."

The green goop on the floor dispersed, and above them two cocoons gave way as the two princesses fell to the ground

"We won, we finally won." Twilight breathed a sigh of relief

"And that does it for me" the Doctor said, "I'll drop off the queen and be on my way."

"Where will you go?" Starlight asked, "Why not stay here?"

"If there's danger I'll arrive" the Doctor looked to the TARDIS, "But the TARDIS is my home, and it's the last piece of my home planet I have left."

[…]

Celestia and Luna woke up to find a note on the throne

You're welcome

-the Doctor