Doctor Whooves: The Adventure Continues

by Draconaquest

Rating: teen
Tags: Equestria Girls, Comedy, Adventure, Crossover, Doctor Whooves, Sunset Shimmer, Twilight Sparkle, Drama
Length: 6278

The Doctor is back, and he must stop a Zygon disease from killing everyone on Earth. With Twilight Sparkle, and Sunset Shimmer at his side, the Doctor has just thiry-six hours before the disease kills him, and everyone on the planet.

While it's only been five months for Twilight, but for The Doctor, it's been two years. Now he's returned to Equestria and is back as the 10th Doctor, and Twilight is very glad to see him. Looking for a break from her royal duties, The Doctor takes Twilight to where he comes from, which just happens to land at Canterlot High. But, the vacation is cancelled when a student is dead with a strange virus of Zygon origin. With the help of Sunset Shimmer, The Doctor and Twilight must save all mankind from the fatal Zygon disease.

Published 2015-01-04 05:30:03 UTC
Last updated 2015-01-04 05:30:03 UTC

On a Warm Summer's day...

Summer in Equestria is always beautiful. The birds chirp in their nests, and soar through the sky to greet the morning. Pegasi wake up and control the weather, eliminating the clouds and making the sky blue. On a rare occasion, a storm must be created, to help water the crops for Earth ponies. This was one of those rare occasions.

"Why are we making a storm again?" Rain Drops asked her boss, Rainbow Dash.

"Applejack has ran out of water, and needs more." Rainbow Dash replied. She placed another cloud onto the large storm cloud. "After all, no water means no apples. And, no apples means no cider. I don't know about you Rain Drops, but I can't wait for cider season."

"That's not for two more months ma'am." Rain Drops relied.

"I know, but I still can't wait for it." Rainbow said. She looked at the amount of clouds she had piled up. "That she should be enough. I'll give Twilight the all clear." Rainbow flew to around the large cloud.

"Are you sure it's a good idea to have Princess Twilight control the weather?" Rain Drops asked. "She's the princess of friendship, not the princess of weather."

"Twilight said she wanted to help in anyway she could." Rainbow explained. "I figured it be a good idea to have her control the weather for a bit. Also, I can't wait to see the look on her face when she fails."

Rain Drops still had a concerned look on her face. "If you say so ma'am."

Rainbow Dash looked around the could, and saw Twilight. Rainbow waved her hoof, giving Twilight the all clear.

Twilight glanced at the cloud, then back at Rainbow. "How do make it rain again?!" She shouted.

"Just kick the cloud with you're back legs!" Rainbow shouted back.

Twilight still looked nervous. She flew up to the cloud and turn around. She gulped, and kicked the cloud. Rain started pouring from it. However at the same time the rain started, Twilight's wings closed. She fell to the ground with a large splat!

Rainbow landed next to her. "You really need to work on your flying." She held out her hoof. Twilight took it and stood up. "Don't worry Twilight, I'm free tomorrow. I'll meet you at my home at twelve o' clock for a flying lesson."

"Thanks Rainbow." Twilight said. She looked at the pouring cloud. "So how'd I do?"

"Not bad for a newbie." Rainbow said. "But, you need to learn to control your wings better. When you kick a cloud, you need ot keep your wings flapping, otherwise you'll fall."

"Yeah..." Twilight chuckled. Then, she heard something. A groaning, screeching sound. A sound that she had not in a long time.

"Is that what I think it is?" Rainbow asked.

"I think so." Twilight said excitedly. She extended her wings, and quickly took off, and flew toward her castle as fast as possible. She was so excited, she could barely contain it.

She barged through the doors of her castle. What she saw brought joy to her heart. A tall blue box with the words Police Public Call Box engraved in light. The light stopped flashing, and the sound ceased. The doors opened and a pony stepped out. Twilight recognized him instantly.

The Doctor stared at Twilight, with a huge grin on his face. "See, told you I'd come back"

A Reunion

"Well, you've certainly been busy." The Doctor said, sitting in a chair next to Applejack's throne in Twilight's castle. "How long has it been since you last saw me?"

"It's been about four months." Twilight replied.

"And, in that time, you've become an alicorn princess?" The Doctor asked.

"I actually became a princess on the day you last saw me." Twilight said.

"Wow." The Doctor replied. "Who knew things happen so close to each other?"

"It certainly amazing." Twilight said.

The Doctor looked around the throne room. "So, when did you get a castle?" He asked.

Twilight sighed. She had a look of sorrow in her eyes. "Um... a couple weeks ago a centaur named Tirek tried to steal all of the magic in Equestria." Twilight explained. "I absorbed all alicorn magic to try and save it. What ended up happening was sad, beyond belief. Upon encountering Tirek, he destroyed the library and absorbed my magic. Using a chest we found, we defeated Tirek. The chest then soared into the air, into the ground and then created the castle."

"That's quite a story." The Doctor said. "Also, I'm sorry."

"Oh, it's fine," Twilight replied. "After all, all good things must come to an end. And when we loose something, something great always guaranties to come in it's place."

"That is very true." The Doctor agreed.

"So, where's Rose?" Twilight asked.

The Doctor's grin sank into a frown. "She's...uh...gone." He said.

"What do you mean?" Twilight asked.

"She's in another universe, with a copy of me." The Doctor replied.

"Is she happy?" Twilight asked.

"I would hope so." The Doctor said. "Anyway!" The Doctor hoped to his hooves. "Come on, your majesty, up, up, up!"

"Why?" Twilight asked, standing up. "Where are we going?"

"Just follow me!" The Doctor said and ran to the TARDIS. He unlocked the door, and ran in. Twilight walked in and saw The Doctor fiddling with the controls. Twilight was happy to see the TARDIS again, especially in this condition. The last time she saw the TARDIS interior, it was practically destroyed.

"So where are we going?" Twilight asked.

The Doctor turned toward her and flashed a grin. "Well, you've seen my world, so I figured I'd show you mine." He pressed a couple more buttons and when pulling a lever he shouted, "Allons-y!" and the TARDIS began to rock back and forth, as it entered the time vortex.

The Crying, The Crime, and the High School

The TARDIS stopped shaking. Twilight opened her eyes. The TARDIS was the same, but she didn't feel the same. But, she had felt this feeling before. She saw a hand stick out in front of her. The hand belonged to a man in a brown pinstripe suit, a light blue shirt, a brown tie, and a long brown trench coat. His hair was sticking up and he had a huge grin on his face. Twilight realized it was The Doctor.

She took his hand, and he helped her stand up. "Easy now," The Doctor said. "It will take a while to get used to new legs."

Twilight cocked her head to the side. "No it won't." She said.

The Doctor had a confused look on his face. "What do you mean?"

"I've been like this before." Twilight replied.

"Hm." The Doctor mumbled. "Well then, maybe you'll recognize this place then." The Doctor walked over to the door and open it. Twilight walked through and entered the bright sunlight. She was looking straight at a mirror.

"It's just a mirror." She said. The Doctor walked out, and shut the door behind him.

"Oh right, sorry." The Doctor said. "Look behind the TARDIS."

Twilight turned around and saw Canterlot High, looking like it always did. "I've been here twice before."

"I thought so." The Doctor said, walking up behind Twilight. "Wait, that's not right." He walked over to the school. Twilight realized that several cars with flashing lights were parked in front of Canterlot High. She hurried to catch up to The Doctor.

The Doctor walked past the police officers holding up a leather flap with a piece of paper on it and said, "John Smith, detective, and this is my assistant Twilight Sparkle. What's going on?"

The officer replied, "Well sir there's been a murder."

"A murder?" Twilight asked.

"That's right ma'am." The officer replied.

"What kind of murder?" The Doctor asked. "Where is the body?"

The officer shifted his footing. "It's inside, sir." The officer replied. The Doctor turned around and walked toward the school. "But, I will tell you, we already have a detective on sight."

The Doctor turned around. "Really, who?"

Sunset Shimmer knelt down to look at the evidence. The body was a pale green, with severe scratch marks on the neck. His forehead had streaks of blood on it. But other than that, he looked fine.

"So, what do you think Ms. Shimmer?" Officer Fox asked.

Sunset stood up shrugging her shoulders. "I'm sorry, but I've only been taking a medical class for the past few weeks, I don't know what to make of the body." She said, scratching the back of her head. "Although, I can tell you that nothing like this have ever been recorded before, at least not to my knowledge."

Fox raised an eyebrow. "Not to your knowledge?" He asked.

"Like I said, I've only been studying medicine for a few weeks, so I don't know much." Sunset confessed.

"Ms. Shimmer, you are the only medical student in this school, do I need to call a doctor?" Fox asked, raising his voice.

Before Sunset could respond, a voice from down the hallway said, "The Doctor is already here." A tall thin man in a pinstripe suit and trench coat was walking toward them. He turned to Sunset. "Hello, I'm The Doctor." He said. "I understand you're a medical student?"

"Yes, but..."

"Great, I could use your help." The Doctor looked to his left, and pointed his thumb at the police officer. "Twilight, could you make sure he doesn't get in the way?"

Sunset looked to her right and saw Twilight walking up. "Twilight?"

"Sunset Shimmer?" Twilight asked gleefully. "It is you?" The two hugged each other and began to ask questions.

Twilight went first. "How've you been?"

"You already know that, I write you every week."

"Yeah, but it's better to ask you in person."

"I've been doing fine. People are beginning to like me more."

"How is everyone else doing?"

"They're doing great. We've all been getting along well. Our band will even go to some other schools and perform."

"That sounds like fun. Where are they?"

"School was called off due to the murder. All of the students wet home. With me being the only member who is taking a medical class, I was asked to see what I could figure out."

The Doctor interrupted the conversation. "Could someone help me please?"

Sunset turned to The Doctor. "Oh yeah, sorry." She walked over to The Doctor.

"Don't be, you were just catching up with a friend." He replied. "I know what that's like. Can you grab his legs?"

"Sure." Sunset said. She picked up his legs, while The Doctor grabbed his shoulders and carried the body into the lunch room.

They set down the body. The Doctor threw his coat aside and put on his glasses. He pulled out his sonic screwdriver and scanned the body. "It's a poison." The Doctor said.

"What do you mean?" Twilight asked.

"I've seen this before." The Doctor said.

"When?" Twilight asked.

"Not for an age." The Doctor explained. "And, I actually wasn't there to see it. Sunset, do you have a computer?"

"Yes, why?" Sunset asked.

"Look up U.N.I.T." The Doctor said.

"I can't."

"Why not?"

"No internet access." Sunset said. "Not with school internet, anyway. I need unblocked internet source."

The Doctor thought for a minute. "Is there a cafe around here?"

"There's a Burger King down the street." Sunset said.

"Great." The Doctor said. "We can get some lunch, as well and information."

"But, what do we do with the body?" Twilight asked.

"Give it to the police, I suppose." The Doctor said. "There's nothing to be done. He's dead, and he can't be brought back."

The three left the building and gave the body to the police. "Just one question: What was the boy's name?" The Doctor asked.

"William Chesterton." Officer Fox replied.

"Chesterton..." The Doctor recognized that name. "What are his parents names?"

"Ian and Barbara." Fox said.

"Are they still alive?" The Doctor asked.

"Yes sir, they live at Cambridge." Fox said.

"Wow...thank you, Mr. Fox. " The Doctor said and walked away.

"You acted like you knew them." Twilight said, as she, Sunset, and the Doctor walked down the street.

"I did." The Doctor explained. "Ian and Barbara Chesterton were some of the first companions that I ever traveled with. Though I didn't know that they were married."

"Really?" Sunset asked. "You know, you haven't exactly explained who you are yet."

"Trust me, you wouldn't believe me." The Doctor replied.

"I'm from Equestria too." Sunset said.

"What?" The Doctor asked.

"I'm from Equestria." Sunset explained. "I left several years ago. I was a student to Princess Celestia, just like Twilight, but I had different motives. I just wanted power, and when it wasn't given to me, I fled to this world. I ended up practically ruling the school. A few months ago, I went back to Equestria, and stole Twilight's crown. Twilight followed me here, and when I put on the crown, I turned into a raging she-demon. Using the Elements of Harmony, I was defeated, and underwent a complete personality change. I swear to you, I'm completely different."

"You even help defeat the Sirens last time I was here." Twilight supported.

"If you say so." The Doctor said. "I suppose I should tell you who I am."

"It would be preferred." Sunset said.

"I'm the Doctor. I'm a Time-Lord from the planet Gallifrey in the Constellation of Kasterborus. I am nine hundred and five years old. I stole a Time-Machine from my people and have never returned."

"I don't know which one of us has a weirder back story." Sunset said.

"Probably me." The Doctor said.

Lunch and the Plan

"Here's your meal sir, that will be thirteen dollars." The cashier at Burger King said.

The Doctor paid, and walked over to the table Sunset and Twilight were sitting at. The Doctor sat down and passed out burgers. "Is this meat?" Twilight asked, pointing at the burger.

"Yeah." The Doctor said. Twilight gagged as Sunset took a bite out of hers, trying not to get crumbs on her laptop.

"Gross." Twilight said, and set her burger down.

"Just try it, you might like it. I did." Sunset said.

"I'm good, thanks." Twilight said.

"Then try the chips." The Doctor said.

"I thought they were called French Fries." Sunset said.

"Depends on where you are." The Doctor said. He turned his head to Twilight. "Go on, try them."

"What are they?" Twilight asked.

"Potatoes." The Doctor replied.

"Oh, I'm okay with those." Twilight said, dipped her chip into ketchup, and began eating them.

A few minutes later, Sunset said, "I think I found out what the disease is." She looked up at The Doctor, "The password you gave me, gave me unlimited access to UNIT records. I seems that the disease was made by an alien race known as the Zygons."

"Oh no, not the Zygons." The Doctor said.

"You've met them before?" Twilight asked.

"Yep. Big, red, rubbery thing covered in suckers. Surprisingly good kisser. They can transform into any living organism. Human, rabbit, pony, you name it. Met them during my fourth incarnation. They tried to take over the Earth. They failed of course." The Doctor said.

"Well, this disease can infect any Zygon. To them, it's like steroids. It increases muscle power, IQ, even the ability to move faster." Sunset explained, "However, to any other living being, it's fatal. Symptoms include: Green skin, muscle tissue decay, brain cell decay, cracking of skin, and loss of movement. Basically the exact opposite to what helps the Zygons."

"According to Brigadier Lethbrige-Stewart, the Zygons have a cure, but it is unknown, as the Zygons would never give it away." Sunset said.

"So, basically, everyone at Canterlot High is infected with a fatal disease, the Zygons could be impersonating anyone at the school, and we may not be able to find the cure?" Twilight asked.

"It seems that way." Sunset said. "Wait, I just thought of something. The disease isn't just at Canterlot High. We have to assume that the Zygons have multiple bases where they spread this disease. And even if it's just at one place, people travel. They go home, they go out of town, they go to large cities for a vacation. Think about those massive cities that almost everyone goes to. Manhattan, Las Vegas, San Francisco, are popular travel destinations with a lot of people there. This disease could spread across the entire globe, and with it being fatal, every living thing on Earth, except the Zygons, would die..."

"Giving the Zygons control of Earth." The Doctor finished.

"But, if that's the case, we might already be infected." Twilight said.

"No, you can't be." The Doctor said.

"What do you mean?" Sunset asked.

"Both of your DNA is part human, part pony." The Doctor explained. "That clash of DNA makes you immune to the disease."

"What about you?" Twilight asked.

"Oh, I'm infected alright." The Doctor said. "And it's accelerating. I can feel it in by blood-stream. Apparently, having two hearts makes the virus circulate through my body faster. Within thirty-six hours, I'll be dead."

"But won't you just regenerate?" Twilight asked.

"No. It seems that there are some kinds of diseases even a Time-Lord can't escape." The Doctor said. "But, we need to have a plan." Twilight and Sunset stared at him. "What?" The Doctor asked.

"You normally have a plan." Twilight said.

"So, just because I normally have a plan, you expect me to have a plan?" The Doctor asked.

"Pretty much." Twilight said.

"Well, in that case you'd be right." The Doctor admitted. "I have a device on the TARDIS that should be able to find a Zygon living amongst us. Once we find the Zygon, we can have it lead us to it's ship. After that, we can find a cure and inject it into the TARDIS which can spread it across the atmosphere, curing everyone on Earth, even the Zygons."

"How can you be sure that there would even be a cure on the Zygon ship?" Sunset asked.

"Because," The Doctor explained, "If the Zygon disease were to combine with a disease from this planet, it could become fatal to the Zygons. If that was the case, you'd want a vial of the cure to save you from that disease."

"Good point." Twilight said. She looked out the window. The sun was setting. She looked at the clock. It was nearly 8:30. "Wow, time flies doesn't it?"

"It does in the TARDIS." The Doctor said smirking. "Anyway, we should get some sleep. Tomorrow will be...interesting."

Staying up Late

The group ended up going to Sunset's apartment. It wasn't the largest space, but it was well kept and clean. Upon entering, Sunset gave them a tour. "The kitchen is to the right, and the bathroom to the left. The fridge is pretty much stocked. If you need a snack during the night, like I normally do, there's a cupboard with some crackers. The dining room is just beyond the kitchen. The living room is forward. The TV has cable, and I have some episodes of Star Trek if you want to watch them. My room is just over there. If you need me for something, just let me know."

The living room was nice and cozy. There was one couch, and two chairs. "You can have the couch." The Doctor said to Twilight.

"I was going to let you have it." Twilight said.

"No, please, I insist." The Doctor said.

"If you say so." Twilight said.

Sunset and Twilight changed into their pajamas, while The Doctor moved the TARDIS closer to the apartment complex. At about 10:00, they went to bed. Sunset had rolled out a sleeping bag for The Doctor to sleep in.

At about one in the morning, Sunset walked out of her room for her usual snack. As she exited her room, she saw the door leading out of the apartment close. She grabbed a cracker, put her jacket on, and walked outside.

She saw the TARDIS, and noticed the door was slightly open. She walked inside, and was surprised to see that it was bigger on the inside. She leaned in the entry way. The Doctor was at the control panel, constructing something. He had changed clothes, as he was wearing the same suit, but he was wearing a blue polo shirt, with a brown t-shirt under it. He looked over to the entry way, and noticed Sunset. He set down what he was building. "It's called the TARDIS." The Doctor said. "It's the time machine I was talking about. It can travel anywhere in time and space. I've had many adventures in here."

"It's nice," Sunset said, "But it's a bit dirty."

"Gee, thanks." The Doctor replied. He turned back to the console, and picked up what he was building. "You're welcome to come in."

Sunset walked in, and looked around. It was a very...intriguing...room. "What are you building?" She asked.

"It's a Timey Whimey detector." The Doctor replied.

"A what?" Sunset asked.

"Sorry, it's the mark four version. I can't remember what happened to mark three." The Doctor said. "What it does, is detect shape-shifting DNA, and dings when it finds it."

"So it's a ding machine." Sunset said, leaning on the console.

The Doctor smiled. "Yeah, I guess you could call it that, yeah."

"So this will help us find the Zygon?" Sunset said.

"By rights." The Doctor replied.

"Well we can only hope." Sunset said. "I have a question."

"Yeah."

"Are me and Twilight actually infected with the disease?"

The Doctor set down the Timey-Whimey detector. He looked at his feet, then back at Sunset. "Yes. I didn't think so at first, but when examining your DNA, I discovered the virus. Your anti-bodies hold most of it off, but the virus is still spreading. You have more time than, normal humans, but you are infected, never the less."

Sunset looked down. "I thought so. Listen, Twilight trusts me. I'm her friend. I hope you can trust me too."

She walked around the controls, and to the exit. "I can't." The Doctor said.

"I beg your pardon?" Sunset asked.

"I can't trust you." The Doctor confessed.

"Why not?" Sunset asked.

"Oh, I think you know why." The Doctor said.

"I'm sorry, I don't." Sunset replied.

"How stupid, do you think I am?" The Doctor said, raising his voice. "I noticed as soon as you entered the TARDIS."

"Noticed what?" Sunset asked.

The Doctor picked up the Timey Whimey detector. "Did I forget to tell you? This is working, and I scanned you as soon as you walked in. Let's just say, I won't need this anymore." He chucked the machine at the floor, as it broke into a million pieces "I don't need to go the school to find a Zygon." He pulled a lever on the console, closing the door. "The Zygon, is right here."

Suddenly, Sunset lunged at him, trying to grab his neck. The Doctor fell on the floor, Sunset trying to strangle him. He reached for a piece of the Timey Whimey detector. He grabbed a small chunk of metal, and swung it to her face. The Doctor stood up, and ran to his tool kit, which was lying on the floor. He grabbed a small metal cylindrical object, with an orange light on it. He activated it at Sunset.

Sunset shrieked in agony, as the machine emitted a pulse in her brain. She fell to the floor, screaming, "Stop! Stop! I'll tell you anything!" The Doctor turned it off and walked over to the person.

"How long have you been impersonating her?" The Doctor asked, his voice fierce with anger.

"Since she walked outside to the TARDIS." The fake Sunset replied.

"Where did you take her?" The Doctor asked.

"To our ship."

"Where is your ship?"

"Oh, so many questions..."

"WHERE IS IT?!?!"

"It's underneath the school."

"Right then," The Doctor said. "Take me to your leader."

The Zygon Ship

Sunset awoke covered in some weird kind of plant. It was like red vines with webbing in between them. It the smell was terrible. She tried to figure out what happened last. She walked outside to see why The Doctor left, when she felt a sting in her neck. Then she passed out, and woke up here.

Her arms were lifted up, and chained up. Sunset couldn't see anything beyond the strange plant. She heard a voice speaking.

"Sir, the agent has been captured." The voice said. The voice was deep and raspy.

"That fool!" A second voice said. "He couldn't protect himself from a simple means of detection!"

They must be Zygons. Sunset thought. Then I must be on their ship.

"Do we know who captured him?" The second Zygon, who Sunset assumed was their leader, said.

"We, uh, believe it was The Doctor." The Zygon lieutenant said.

The Zygon commander slammed his fist onto a console. "Why is he always here?" The commander asked himself. "Where is he now?"

The lieutenant checked the data pad he was holding. "He, our agent, and the blue-haired female are heading directly to us."

"How long until they get here?" The commander asked.

"Approximately, twenty-seven minutes, and thirty-six seconds." The lieutenant said. "We don't have much time to prepare. What are your orders, sir?"

"Accelerate the disease." The commander said.

"Pardon me for asking, sir, but isn't that dangerous?" The lieutenant asked.

"Extremely." The commander acknowledged. "It could cause damage to us. But, what choice do we have? Besides, The Doctor's biology is different from human biology. His biocardiovascular system makes the disease travel faster through his body, doubling the time it takes for humans. Do we know when he arrived?"

"According to the security cameras, he arrived twelve hours ago." The lieutenant said.

"That leaves about twenty-four hours left." The commander estimated. "What is the maximum we can increase the disease by, without causing damage to ourselves?"

"Times fifty." The lieutenant said.

"Then increase it by forty-eight." The commander said. "That gives The Doctor about thirty minutes to live. Make sure he gets here before he dies. I want to see the Time-Lord breath his last breath."

See the Time-Lord breath his last breath? The Doctor. They were going to kill The Doctor. That also meant that Sunset most humans has one hour to live. Sunset needed to escape, and find that cure. And fast.

"Sir, may I ask why we have the cure to the disease, when it's not deadly to us?" The lieutenant asked.

"Because, if the disease mixes with an Earth virus, even a small one, it could become fatal to us." The commander explained. "The cure should cure us of both our disease, and the Earth disease. If fact, I'd like the cure moved to my quarters, for safe keeping."

"May I ask why?" The lieutenant asked.

"So, I can keep my eye on it." The commander said. "Now, increase the disease by forty-eight times, and move the cure to my quarters!"

"Yes sir!" The lieutenant shouted and hustled away.

Now Sunset knew where the disease was, but couldn't get to it. Not while she was covered in this plant. Her only hope was that The Doctor and Twilight got here quickly.

The Cure

"AARGGHH!" The Doctor exclaimed, as he fell on his knees in pain.

"What is it? Are you alright?" Twilight asked, getting on her knees.

"The Zygons have accelerated the disease." The Doctor said, still in pain. "They probably just did it to kill me. Judging by how must pain I'm in, I'm guessing I have half an hour to live, at most."

"How far are we from the Zygon ship?" Twilight asked the fake Sunset Shimmer.

"It's right in front of you." She replied.

"I don't see anything." Twilight said.

"That's because it's cloaked, stupid." The fake Sunset replied.

The Doctor stood up, still in pain, and pulled his sonic screwdriver out of his suit jacket. He pointed it directly in front of him, and pressed the button. Suddenly, a large ship appeared, flashing with light. It now looked translucent, like you could see it, but you could still see through it.

The door opened, and Twilight could now clearly see into the ship. Upon entering, The Doctor whispered to Twilight, out of the hearing range of the fake Sunset. "Sunset is probably off to the side, covered in a Zygon web." He handed her his sonic screwdriver. "Take this, it's preset, so you'll be able to unlock the chains that's holding up her arms. After that, see if she knows where the cure is. Zygons have a tenancy to speak of their plans aloud, so she might know where the cure is. If she does, both of you go where it is kept. Once you find it, run to the TARDIS as quick as you can. Insert the cure into the console. I set up a program so it will release the cure into the atmosphere."

"What happens if Sunset doesn't know the location of the cure?" Twilight asked.

"Then just search the ship for the cure." The Doctor said.

They walked into a large room. Several Zygons were at consoles. They were uglier than Twilight expected. She looked around the room trying to find Sunset. She saw a weird web. At the bottom of it she saw purple slippers, with legs extending out of it. She walked slowly to it.

A Zygon walked up to the fake Sunset and said, "Agent, you have failed in your duty."

The fake Sunset straightened. "Agreed sir." She said.

"Revert to your natural form." The commander ordered.

The false Sunset reverted back to Zygon form. The commander walked over to a console, and pressed a button. A laser beam appeared out of the ceiling, and struck the false Sunset. It screamed it agony, as it was vaporized, and exploded into ashes.

Anger appeared on The Doctor's face. "You didn't have to kill him!" He shouted.

"He failed in his duty. The consequence is execution." The Zygon commander said.

"He failed slightly!" The Doctor shouted. "Besides, for you, it was a good thing. You want to see me die, and by him bringing me here, you might just be able to do that!"

"What's done is done, Doctor!" The commander shouted back.

"No, you know I'm right." The Doctor shouted back.

Twilight removed to web off of Sunset. "Twilight!" Sunset said happily.

"Shhh!" Twilight said, and used the sonic screwdriver to remove the chains from Sunset's wrist.

Sunset hopped down and whispered, "I know where the cure is. It's in the commander's quarters."

"Great." The two tip-toed to the commander's quarters, and entered it. Luckily, all the Zygons were watching their commander argue with The Doctor.

Resting on the captains table was a glass case with a vial of purple liquid inside. The case was held to the desk by four locks. Twilight walked over to it, while Sunset guarded the door. Twilight tried to use the sonic on the locks, but it wasn't working.

"It's not working." Twilight said, frustrated.

"What?" Sunset asked. "I thought that thing could unlock anything."

"The Doctor once told me that it could unlock anything, except a deadlock seal." Twilight said.

"What is that case made out of?" Sunset asked.

"Glass." Twilight replied.

"Hand me the screwdriver." Sunset said. Twilight gave it to Sunset. Sunset held the screwdriver my the end, raised it up, and smashed the case.

"I guess that works too." Twilight said. Sunset grabbed the vial, and placed it in her jacket.

"What do we do know?" Sunset asked.

"We get back to the TARDIS, as fast as possible." Twilight said.

The two slowly walked out of the room, back onto the bridge. The Doctor and the commander were still arguing. The Doctor noticed them and mouthed, run.

"What?" The Zygon commander asked, and turned around. He saw Twilight, and Sunset, and shouted, "Get them! NOW!!!"

Twilight and Sunset ran to the exit as quickly as they could, avoiding the very slow Zygons. Twilight tossed the sonic to the Doctor, as he collapsed in pain. Two Zygons transformed into humans and chased after Twilight and Sunset.

"You're time is running out, Doctor." The commander said, approaching him. "You only have about five minutes left."

The Doctor crawled to the exit, and pressed the screwdriver against the lock, closing the door. He stood up, and slowly walked to the door, hugging the wall. His body wanted to collapse, but his mind knew he had to escape.

Twilight and Sunset ran as fast as they could to the TARDIS, which The Doctor had moved to the courtyard in front of Canterlot High. They ran, and they ran. Sunset looked behind her, and spotted the human-looking Zygons. "We're being chased!" She shouted, and looked back in front of her. They were just a few blocks away from Canterlot High.

They arrived at Canterlot High, and ran into the TARDIS. Sunset grabbed the machine The Doctor has used against the Zygon, and ran to the entrance while Twilight searched for the place to inject the cure into. Sunset turned on the machine, and the Zygons shrieked in pain. Inside, Twilight spotted the place in the console, and shouted, "Toss me the cure!"

Sunset reached into her jacket, and grabbed the cure. She tossed it to Twilight, who placed it into the console. The TARDIS shook, and rattled, causing Sunset to fall in. The doors closed, and the TARDIS lifted off the ground, spinning into the sky. Inside the TARDIS, the cure drained out of the vial into the TARDIS. Outside of the time machine, purple vapor was released into the atmosphere. It exploded into the air, causing the sky to turn purple for just a minute, before disappearing.

Outside, of the Zygon ship, The Doctor had passed out, and was sweating greatly. He breathed in, and breathed in the cure. He opened his eyes, and wiped the sweat from his forehead. He sat up, and grinned. Twilight and Sunset had succeeded. The Zygon threat was over.

Afterwards

The Doctor entered the Zygon ship, and walked to the bridge. The commander approached The Doctor. "We can still infect you, Doctor." He threatened.

"Oh, don't be so daft." The Doctor said. "It's over. As soon as the cure was injected into the atmosphere, everyone on Earth was cured. And, once I opened those doors, the cure was released into the ship. All of you are cured. Every atom, every molecule, of the virus has been erased. There is no more virus for you to infect people with."

"We're the last Zygons in existence, Doctor," The commander said, "and you've sentenced us to death."

"No I haven't." The Doctor argued, "There is a way. I can take you to an uninhabited world, much like Zygor. You can start again. You don't need to conquer a world to live on it."

"Yes we do, Doctor!" The commander shouted. "We have evolved too much to live on a desolate world. We require a world with advanced technology!"

"I'm offering you a chance to live!" The Doctor shouted.

"Well, we do not accept!" The commander shouted. He walked over to a console and pressed several switches.

A voice rang out throughout the ship: "Self destruct initiated. Thirty seconds to self destruct."

"What are you doing?!" The Doctor shouted.

"If the Zygons are to be extinct, then so will the Time-Lords!" The Zygon commander shouted. The Doctor ran through the ship to the exit. He ran out, and less than five seconds later, the Zygon ship exploded.

The Doctor looked at the wreckage thinking about how he had just caused another species to extinction. And he had even more weight on his conscience.

The Doctor arrived at the TARDIS. Twilight and Sunset were sitting outside it, talking. "So, back to Equestria." The Doctor said, opening the doors.

"Actually," Twilight began. The Doctor turned around. "I was hoping to see some things here. After all, I've been to a lot of past Equestria, and I'd like to see something new. I was hoping to see some of this universe."

"If that's what you'd like." The Doctor said, and walked into the TARDIS. Twilight followed him, and Sunset followed her.

The Doctor took of his trench coat, and tossed it onto one of the structural supports. He began to press buttons on the console, and then turned around. "Yes?" He asked Sunset, who was standing at the entrance.

"I was wondering if I could come with you guys." Sunset said. "I mean, I'd understand if you say no, since I've done some pretty bad things, but I was hoping I could come with you."

"Sunset," The Doctor began, "We've all done terrible things in our lives, myself included. To stop a war, I destroyed my home planet, and all my people. I am alone in the universe, the last Time-Lord. If everyone didn't trust be for that, then I wouldn't have a purpose in life. I trust you, and I hope that you trust me. Of course you can come."

"Really?" Sunset asked, excitedly.

"Really." The Doctor confirmed.

"Oh, thank you!" Sunset shouted.

The Doctor walked around the console. "So, have either of you ever been to New York?"

"No." Twilight and Sunset said.

"All right then, New York. Let's say twenty thirty-three." The Doctor pulled a lever on the console, and the TARDIS disappeared into the time vortex.