They all walked outside the TARDIS to see they had landed in Ponyville. One thousand years in Ponyville's past, but Ponyville nonetheless. "I recognize this!" Duskshine exclaimed. "History books say that this was the day Celestia and Luna defeated Discord- DUCK!"
They all ducked just as what seemed to be a bolt of magic flew over their heads and into a tree. When it made contact, the tree withered into nothing. As they stood up, Bubble Berry came to a sudden realization. "Doctor, did you say you were nine HUNDRED years old?!"
The Doctor replied. "Yes, but is that important at the moment? A laser beam of death just flew over our heads! It seems we're in a warzone! DUCK! AGAIN!"
They did as he said, only to see the magic bolts coming from both ends of town.
"Well," the Doctor stood up. "Let's investigate! Allons-!"
Duskshine pulled him back down. "Are you stupid?! Did you see what that bolt did to that tree? As long as we stay here and duck, we'll be safe!"
The Doctor refuted, "Oh, but what kind of fun is that?"
Duskshine retorted, "The kind that keeps us aliv-"
A voice cut off the rest of his sentence. "Discord! For your crimes against the whole of Equestria, you will surrender!"
"That's Celestia!" Duskshine exclaimed as the holder off the voice walked over to where the Doctor and company were ducking, followed by a pony who was as dark as the night.
The one presumed to be Discord casually strode to meet Celestia. "Oh but Tia, where is the fun in that? Oh never mind! I have a friend that I would like you to meet! He just fell out of the sky, and I HAD to take him home! Come on out Bilbo! I named him Bilbo, by the way."
The Doctor's face flushed with fear as 'Bilbo' rolled around the corner and said, "Exterminate!"
The Doctor yelled, "Everyone! Back away! DO IT NOW!"
"What's wrong?" Duskshine asked.
"That... that is a creature bred for war. It is a Dalek. It only wishes to destroy any and all things that are not Dalek. Especially me. It's only instinct is to kill. It feels no emotion, no remorse."
"Oh," Butterscotch spoke. "it can't be that bad! I'm sure all it needs is a little kindness!" He went and touched Bilbo's outer shell. "OW!" He cried, for the outer shell of a Dalek burns all who touch it. It left a red hoof mark from where he touched.
"THE DOCTOR!" The Dalek said. "I have finally found the Doctor! The Doctor must be Exterminated! And any who travel with him!"
The Doctor responded quickly, hoping to buy some time. "WAIT! Wait! Before you exterminate all of us, please humor me and answer something. How did you- on second thought, you seem to always survive, so I give up asking. But how did you find me? And how many are you?" He asked.
The Dalek answered. "A dimensional rupture in the space-time continuum allowed me to track you to this spot."
"The jump from the parallel reality! OF COURSE!" The Doctor exclaimed. "Now, how many are you?"
Bilbo paused and lowered his eyestalk. "... I am the last of the Dalek."
The Doctor stood up and smiled. "Oh-ho-ho! Isn't this just brilliant! The last of the Daleks before the last of the Timelords! And I know, that under that emotionless flesh and steel one emotion still remains when you see me. And it's fear. You fear me."
"I must obey orders! I must Exterminate the Doctor!" The Dalek aimed it's arm at the Doctor.
"BUT WHY!" The Doctor shouted. "All the Daleks are dead! What is the point of it anymore?!? You HAVE no orders!"
Bilbo paused. "...Then order me to die."
The Doctor denied. "...No. I WILL NOT commit a genocide by killing the last of the Daleks. If you look genocide up in a dictionary, you will see a picture of me and a caption that says 'Over My Dead Body'. There's another way. There's always another way."
Discord yawned. "This is becoming dreadfully boring. Bilbo, dispose of one of the Princesses."
"Exterminate!" The Dalek replied. He shot a beam from his hand and straight into the princess that looked like the night. She screamed in agony as she glowed green and her skeleton could be seen for a split second as she collasped.
"LUNA!" Celestia yelled as she rushed to her sister's side.
"Dear sister..." Luna breathed. "...forgive him..."
"Everthing is going to be all right. Hang in there sister." Celestia's horn glowed. There was a bright light, and when it dispersed, Luna was gone. Celestia turned to Discord, filled with unbridled rage. "YOU! Not only have you murdered my subjects, you have taken my only sister away! Oh, but she will be fine! I sent her to the moon! She draws power from it! It may take one thousand years, but she will be okay!" Tears started falling from her face as her horn glowed. "YOU... WILL... DIE..." She held Discord in place with her magic.
"NO!" The Doctor stopped her. "There's another way! There's always another way!"
Discord yawned again. "Bilbo? Would you kindly finish them?"
"Exterminate!" But the Dalek didn't fire. "What is this feeling? Why can I not Exterminate them? Daleks do not 'feel' emotion. What is happening? Explain! Explain!"
The Doctor smiled. "I see what happened. When Butterscotch touched you, he infused his DNA with yours. Now, you physically can't, because it happened to be fused with the DNA with the kindest creature I have ever met." Butterscotch blushed.
"In other words," Duskshine added. "You are learning the magic of friendship!"
"This cannot be!" The Dalek said. "Daleks cannot learn this 'friendship'!"
Discord looked unamused. "Well, how can I take over Equestia with something that won't fight? Bilbo, I am terribly sorry to say this, but, your services are no longer needed... Kill yourself."
"NO!" The Doctor yelled. But it was too late. The Dalek ended it's own life with an explosion. The Doctor was speechless. He turned to Discord and started running. Celestia pinned Discord to the ground with her magic. The Doctor reared up on his hind hooves in order to deliver a blow that would surely end the draconequus' life.
But instead, he lowered himself and spoke in a thunderous tone. "I cannot and will not end your life, because that is not the man, or colt, I am. I never would. And you," he turned to the Princess. "you make sure you build this kingdom on the concept of one that never would. If you do not," he threatened. "the fury of a Timelord is a terrifying thing." He turned toward Duskshine and his friends and spoke to them as he walked towards the TARDIS. "Let's go."
"Oh, but where is the fun in that?" Discord said as he shot a beam from his hands that hit the Doctor square in the back. The Doctor collasped.
Duskshine gasped as he and his friends rushed to the Timelord's side. "Doctor..." He breathed. "Doctor! Come on! Wake up, Doctor! ...I need my Doctor!" He glared at Discord and yelled. "What have you done?!?"
Discord smiled. "Well, I shot a beam from my hand. It hit that pony. AAND It should have killed him. Looks like it worked too! Multa Bene!"
Duskshine and friends look down on their time traveling friend in despair. Bubble Berry mourned. "I wanted to throw him a party..."
"That monster..." Elusive whispered.
"Doctor..." Rainbow Blitz silently said.
"He can't be dead, he just can't be!" Applejack stated.
Butterscotch, normally well-tempered, exploded as he walked towards Discord. "YOU MONSTER!" He continued to speak, but as he did, he began to glow and his voice became somewhat distorted, somewhat god-like. "How could you do that to the Doctor! He didn't do anything! He was just a lonely traveler! And even after sparing your life, you killed him!" He yelled out in frustration and his eyes oscillated with white light. The other colts had begun to do the same. They had also begun floating as waves of pure energy rotated among them.
Duskshine spoke as he floated. "For shedding the innocent blood of a traveler and our friend, YOU... WILL... PAY."
Discord looked scared. "Wha- what is that?"
Then, a wave of all colors exploded from the six ponies and enveloped Discord. He screamed as it washed over him. When it finished, Discord was nothing but stone. As the energy faded, the colts fell to earth with a thud.
Duskshine rubbed his head and said, "What a trip... Wait, what's this?" He saw something that wasn't there before the final attack. Six stones that held imprints of the colts' cutie marks sat in a pentagonal shape, with the one containing Duskshine's cutie mark in the dead center.
Celestia spoke to him. "Those stones were created through the immense amount of energy you created with that blast. And yet... Still a great energy is emanating from them. We must keep them safe, so that no evil may use them. I shall name them the... Elements of Harmony, because they were used to stop Discord, the opposite of Harmony."
Duskshine smiled. "Sounds good."
"Woah..." The Doctor sat up. "add 'getting hit by a magic beam' to the list of things that I do NOT want to do again. What did I miss?"
"DOCTOR!" The six colts shouted in unison.
"Well," The Doctor started. "how about we get you back in your time. Allons-Y!"
The six friends began laughing hysterically. "What?" The Timelord asked.
They continued to laugh. "What?" He asked again.
"You missed the most important part!" Berry said.
"WHAT?" The Doctor asked.
"We'll tell you all about it along the way." Rainbow Blitz said in between his laughter.
"...WHAT?" The Doctor asked as they all piled into the TARDIS.