Alright, I think I'd better explain what's going on. My school required my to do an intersession project, and I've been getting into other stuff, so this is a bit late.

on that note, I think that Dr whooves is to be an open-ended show, where there is not set release day of episodes. Enjoy!

A man sat in a chair, facing a sontataran general. The sontaran was in standard military dress, as befitting to the clone race. The man was dressed in a WWII greatcoat. "Captain Jack Harkness, we have received reports that rutian scum has plotted to infiltrate a planet called Equestria. The success of your mission will determine the survival of the clone race." Harkness knew that the sontatarians were forever at war with the rutian host. They were pretty committed, a clone army forever in battle with the rutians.
The immortal shrugged. "What does that have to do with me?"
"As our honor code states that we do not kill an innocent, we have delayed the invasion, which our mathematicians deuce there will be many civilian deaths, by sending a fireteam of detectives to the planet. You will lead that fireteam. Your mission is to find whatever the rutian host is up to and stop." Harkness knew that the entire law system, the entire society of the sontatarian clone army was based on honor: a clone would rather commit suicide rather than dishonor himself on the field of battle.
"Who else will be on this fireteam?"
"Ah, Yes, Captain Harkness. You might know him. Or one of them, anyway." Jack turned around, and heard the sounds of a TARDIS materializing.
"You've gotta be kidding me." Imagine Jacks surprise as he saw the TARDIS, the blue box. Imagine his greater surprise when he saw the Doctor and his new companion as a pony!
"Jack! Been a long time!"
"Uh...yeah...I guess..."
"Well, I suppose we've got to get a move on. Our coordinates are a concert in Canterlot, where rutians are planning to have a sort of conference, someone where no one would find them. Hidden in plain sight."
While there were in the TARDIS, the Doctor talked to Jack. "I'm so sorry."
"Who told you?"
"Gwen. During the brief Ice warrior-human war. It was my fault that it had to be that way. I read the reports. The 456-"
"So, hows it been?" said Jack, changing the subject. "New body!"
"Oh, yeah, the regeneration!" Jack was an old friend of the Doctor's: they had met in his ninth incarnation, but when he regenerated into his tenth, he left Jack on platform one. Jack used a vortex manipulator to travel to 21st century Cardiff (knowing the Doctor would be there), but he landed 200 years short, and had to work for Torchwood, an earthling organization dealing with extraterrestrial threats, but left once to help the Doctor. He left torchwood permanently after his lover, Ianto Jones, Died in the 456 invasion. The last time they met was at a bar in deep space, when the Doctor gave Jack the contact info of Alonzo Frame, a midshipman on the Starship Titantic. They chatted about what had happened while they were apart. "So, where's Alonzo?"
"Dead. Murdered."
"WHAT?"
"Yes. We crash landed in a forest, like a jungle, and these insect-pony-things started attacking us. I barely survived. I was able to fix my manipulator, and returned to Earth."
"Odd. I'm sorry. Alonzo was a nice lad. Very bright."
The TARDIS materialized in a square in Canterlot. "Wait, so this is a planet full of candy-colored, talking, magical ponies?"
"Um...yes Jack. In fact, you're one yourself!"
"Wha-" It was true: he had a blue body, a white mane, and orion on his rump.
"Tell me Jack; do you feel connected to the constellation orion?" A female voice appeared behind them "A hunter with a great aim and everyone talks about his belt? That orion?"
The Doctor spun around to find Ditzy, walking through the door.
"Hey, What's your name?"
"Jack, do not flirt with Ditzy. Or me, for that matter." It was a necessary precaution-Jack was not only bisexual, but omnisexual. No, pansexual. "Were here."
"Doctor-we don't have tickets." The Doctor took out his psychic paper, and showed it to the guard. "I have a season pass." he said to a guard. "Scuse me, Ditzy, but I have to go to the restroom." The Doctor went to the restroom, and saw a pony with green eyes, definitely a rutian infiltrator. Rutians were shapeshifters, which made the Doctor's work even harder. The Doctor took his sonic, and took the signal from the man's ear buds, which the Doctor deduced was a mode of communication between the rutians. He then took out some ear buds of his own, and applied the signal to the earbud.
"This will enable us to hear whatever the rutians are saying." he explained to Ditzy when he was back. The Lights started dimming, and then, they took their seats. The Doctor heard voices on his end of the line, and was shocked at what he heard.
"How goes the infiltration?"
"It goes well. All we have to do is steal the thing. Our operatives are part of the force that guards the thing, and are getting closer and closer everyday."
"What of the Doctor?" The Doctor quickened his pulse. Did they know that he was there
"Oh, Yes, him. We should take him down in the theater. Our agents are rolling smoke bombs in now. We should be able to take him down in the confusion. No one will notice, and people will assume that he was trampled by the crowd." The Doctor got out of his seat.
"We've got to go. Now."
"Why?" But Ditzy was answered, quickly; the smoke alarms went crazy. Several green-eyed ponies drew guns, and shot the Doctor, but it wasn't anything more than a dart. What did the doctor think it was a bullet? It didn't matter then, as Jack tried to charge a rutian, but was shot as well, and Ditzy also got shot. The Doctor blacked out, and just before he went to sleep, he saw Jack and Ditzy fall as well...
They woke up in a hospital. Ditzy greeted the Doctor. "Doctor, you were out for a week."
"Why?"
"Because the doctors had to deal with your time lord body. It took them days before they realised that your regeneration energy was taking out the virus."
"It was a Virus?"
"Yeah; one that seemed to shut down the body systems except for the brain, heart, and lungs."
"Sneaky rutians. Ditzy, what have I said about injuries like this? One of us gets injured; straight to the zero room with them!"
"What did you find?"
"Its about the EERC. About two years ago, they obtained a crucial piece of energy that could turn the tide of the sontaran-rutian war. It also could power all of equestria, and bothe sides have the means to convert it into a deadly weapon. And the rutians plan to attack it. By force."
"EERC?" Jack walked in the door.
"The equestrian extraterrestrial research center, Jack. Sort of a pony torchwood." Jack grumbled at the word. He worked for Torchwood for 200 years, and it wasn't a great start. He began employment strapped to a chair in a dirty cardiff dungeon.
"We need to defend that place, as much as we hate it!"
"I agree. The sontarans are depending on us."
"No. We can't let any side use this energy source as a weapon. And of course the sontarans, a clone race dedicated to war, would use it as a weapon just as much as the rutian host! We have to protect it: from both sides."
"And if we can't, we'll destroy it."
"Agreed. Come on!"
"Where are we going?"
"To the castle."
The Doctor got out of bed, and went out of the hospital. "Wait-straight to the castle? Couldn't it wait?"
"No. Every second we waste, the rutians gain ground."
The guards let them in (the Doctor saved their entire planet from the Daleks, The Autons, Nightmare moon, The Vasta nerada, The windigoes and the guardian of chaos, and the Ones Who Take The Mind, after all) and they entered the main hall. "Princess Celestia, I have come for your help, regarding the Equestrian Extraterrestrial Research Center."
"How do you know of such a place?"
"I have sources." said the Doctor. This was a blatant lie; the Doctor snuck into the facility one time, and he'd rather Celestia not hear it, even if he was trying to save ponykind from a deadly virus. "I need to see the energy source that you captured two years ago. There are forces that attempt to use the source as a weapon, and it is in my interests that I protect it."
"We will do what we can to ensure it is safe, and I know you can make that so." she pushed a button on her throne, and the gears behind them started moving. She hopped off before it opened to reveal the facility. They strode over to a room. The Doctor was pleased that Jack had not flirted with anybody. But that was odd. Jack was a flirter at heart, and if there was a seduction ban, he would rather leave the TARDIS. The Doctor had to keep tabs on Jack.
Striding through the facility, they guards, all with green eyes, opened the door. Within the Door, he found a small cube. He took out the sonic, and performed some tests. "Sure is powerful, but not powerful enough to power an entire armada or invasion force. A flotilla of battleships at most. So why would they try to seize it is it isn't what they wanted?"
"Because It's not what we want, Doctor!" the Doctor turned around, and saw Jack, with electric green eyes, pointing a pistol at him. Behind him were the guards, pointing similar pistols.
"You didn't think that we would track you, Doctor? Follow you? This is a fake. It's really a failsafe generator from the planet Traxian 8, used to power ships. How do you think you were able to find it so easily? We are not stupid, Doctor."
"What have you done to Jack? How long have you been keeping him?"
"Thats for me to know, and you not to find out. You've found out much in your past lives. You screwed us over in London. The gunpowder plot? Won't happen again."
"I'LL SAY IT AGAIN: WHERE IS JACK?!" But the rutian didn't answer, pulling the trigger. The Doctor knocked it out, and then, used the Not-Jack as a pony shield, using him as a bullet sponge. He then ran to the left guard, and knocked him out. That last one pulled out his gun, and shot a bullet towards the Doctor. No one expected Ditzy flying between the Doctor and the bullet to receive the bullet, square in the chest. A blast propelled the guard forward, to reveal the assailant, Celestia. "How is Ditzy?"
"She has moments, if I don't do this. We can't wait for nanogenes. Stand back!" Celestia stood back, and the a light, a dust expelled from the Doctor's hands and Hooves, going into Ditzy's mouth. It then went on to heal her heart, repair her ribs, repairing the skin and her coat. Her eyes shot up. "What happened?" The Doctor Kissed her in the neck. Ditzy started up.
"What's wrong?"
"Doctor-I'm pregnant."
"Who's the father?"
"You."
"But we didn't-"
"I don't know what. But It just happened. When you used her regeneration energy to save me, I received your DNA. My body must have paired it with my own DNA, and I'm pregnant now."
"I'm so happy." The Doctor was going to have a child for the first time in almost 700 years. He'd had seen and experienced so much sadness-the time war, Amy's death, Rory's death, Rose casted off into another universe, Donna having to forget their adventures together, Adric's death, even, that having a child was so happy for him.
"You want to leave the TARDIS-you can, you know."
"I Won't leave for all of Equestria. I'll stay."
"Let's go. Where the rutian flagship is, I don't know. If it's in equestrian orbit, then it has a perception filter, but I doubt it."

Light years away, on Rutia III, Jack Harkness, now human, was chained up to a cross, where wires were running inside his body. Suddenly, an electric shock went through his body. He screamed. "You think we are giving pain, but we are taking something much greater."

The Doctor stepped away from the TARDIS. "Well, we know what We're up against. They don't have a ship in the atmosphere at all. They want him well protected. Thats why they have them on their own planet.
"Why would they need him?"
"They need-oh. When Jack became immortal, he became a living fixed point in time. they must be using his energy as a fixed point in time to spearhead the rutian advance. I've got to alert the sontarans!" The Doctor punched some buttons on the console, and then, a sontatarian appeared on the screen. "Well, Doctor, have you found what we have asked?"
"Well, we assumed that the rutians were searching for a certain energy cube, which can power any machine, large or small. Our assumption was incorrect. They were looking for our third member, Jack Harkness. as he is immortal and a living fixed point in time, he can generate a large amount of energy, which the rutians are sapping at present."
"We will send your report to our leaders on Sontar."
"Thank you." Suddenly, the Doctor felt faint and dizzy. "He's dying, Ditzy. He is becoming more and more mortal, and it's all my fault. And if that isn't the case, then the sontarans will be hunting him down too. Ditzy, we've got to go now."
The TARDIS landed on the bridge of the rutian flagship. "This is the bridge. as the helmsman of the rutian fleet, Jack will be here."
He stepped outside, where the rutians were in front of him. Jack, in his pony form, was stunned, even as he was strapped to a rutian-energy sapper of some sort. He also was growing older and weaker, as if the immortality was breaking. In a heartbeat, the Doctor spun around and tried to demat the TARDIS, but then, a rutian knocked the tool out of his hand. It spun to a halt.
"What?" For some reason, the Doctor pulled a recording device out of his pocket, and clicked record.
"Even though the immortal is a powerful energy source, it has it's limits. The TARDIS has much promise."
"WHAT?"
"Think of the armies that we could summon. Your greatest enemy preceded us, but he released mere toclafane. What if it was greater? What if we could release the Meanwhiles, the Neverwheres, the Nightmare Child and the Could've Been King?"
"No. You can't. Turn the TARDIS into a paradox machine, Release the horrors of the time war, just to stop the sontarans?"
"Why stop with the sontarans? Think of the races we could destroy! The Daleks, the Cybermen-think of the promise!" The Doctor thought of this. it was tempting, saving all those races. But he had an answer, and nothing could change it.
"No."
"NO?"
"The power to destroy the most feared race in the galaxy-people don't need that power. They want it. Need it. Crave it. I had that power, once. In my fourth incarnation. If I connected two wires, I could end the dalek race forever. Wipe it out form all of time and space. Obvious . And when they have that power, they use it for their own ends. No one, NO ONE, will use their power entirely for good. So I say NO. You release my TARDIS." The Doctor stoppe recording, but continued. "Besides, you're signing your own death note. The rassillon imprimatur states that only time lords can use TARDIS's."
"Doctor, you think us foolish enough to-" but he never finished his sentence. A large explosion was heard behind them, taking advantage of the distraction, the Doctor leaped forward, grabbed the sonic demated the TARDIS (with Ditzy in it), and then, switched the sap. Energy surged towards Jack, which also released Jack from his bonds, as well as making another explosion, which resounded across the ship. "A sontatarian battlefleet is attacking!"
"ALL HANDS ON DECK! All remaining power towards the shields!" Another explosion sounded. The Doctor put Jack over his back, and started walking towards the exit. Grunting as he started along, he felt the blood on Jacks body. It wasn't hard carrying Jack; he was all skin and bones. Then, a large explosion rocked the deck, and pieces of shrapnel started flying towards the Doctor. He masterfly dodged all, but one large piece ripped open the hull of the ship, and sent the Doctor and Jack flying into the vacuum of space. The last thing the Doctor felt before flying into the void was Jacks hoof, and the last thing he thought was that he would never let it go.
What did the Doctor feel? Death, explosions, all around him, for sure, but mostly nothing, if you can imagine it. That's what space is: nothing. The sontarans arrived just in time to save the Doctor, but not to save Jack. That was their reason for attacking the Main rutian armada. The Doctor slowly opened his eyes, and saw some contrarian marines point at him and come towards him. He lost consciousness. Again.
His eyes shot up. It was clear he was in a medical unit. He was In a pod, where he assumed that nanogenes were doing the work. When he woke up, He found DItzy standing in front of him. "Where's Jack? How long Have I been out? Also, how did you get out of the TARDIS, and make it pilot here?"
"You were out about...maybe 2 weeks. Apparently the regeneration energy got in the way of the nanogenes, so thats why. Also, your pony form might have complicated matters Jack is just outside of the ward." Of course. Jack would have been up the moment when he was safe. The Doctor got out of bed.
"You're escaping the third question."
"I don't know, but I think my fetus is sharing the time lord DNA with me, enabling me to pilot a TARDIS. I received a tip from Jack that you were here and here I am." The Doctor got out of the ward, where he embraced Jack. "Jack! We made it!"
"Doctor, I was thinking...and I've had two weeks to think about it-but-could I join you?"
"Course. There will always be a place for you here, Jack." They went out the door, towards the TARDIS. But before they could enter, they were approached by the sontarans. "Doctor! We're here to seize the TARDIS and Harkness..."
The Doctor threw the sontarans a data stick and the energy cube, then said, in an unforgiving tone, "Get the fuck out." He slammed the door of the TARDIS, and it dematerialized.