Return of the Master

The TARDIS shook and sputtered, sparks flew, causing the Doctor to stumble away from the controls, knocking over Spike, who ran into the console, making matters worse. "Augh!! Somepony's been messing with my TARDIS!!!" The Doctor screamed. Flipping switches and pushing buttons, the Doctor tried with all of his might to stop the machine, but nothing he tried seemed to offer up any results.

Derpy ran into the Doctor, knocking him off of his hooves, over the side and down to the area underneath the console.

Then, the shaking stopped.

"Oof... Everypony OK? Ow... I think I hit my head..."  The Doctor said, getting a yes from all three of his companions, Spike the dragon, Twilight Sparkle and Derpy Hooves. "Don't touch anything... I'll come up in a second..." The Doctor said as he sat up, and stood on his four legs. "Now then! Why are you making all that ruckus, huh?" The Doctor said as he took out his Screwdriver and rushed up to the console.

"What was that all about?"

The Doctor scanned the console, and found no damage. "Huh..." He scanned more parts of the console, with each time getting more of a confused look on his face. "That- that's not possible. No. No. It-it's dead! The TARDIS is dead... The last one in the Universe..."

"What- What do you mean, it's dead?!" Twilight asked, running up to the brown stallion, who had a grim look on his face. "Are we stuck in Equestria? Not going to your Universe?! What about reality?! It's gonna blow up!!"

"Twilight, there's nothing in this Universe to distinguish the Time Vortexes. They've separated, gone into their respective places. Mine's gone, so no, reality won't blow up." The Doctor laid a hoof on the TARDIS’s console, and shed a tear. "The last TARDIS..."

"Um... Twilight, who is pony? You have't given me a straight answer ever since we met him!" Spike asked for the second time in the TARDIS. Twilight looked to the Doctor for an answer. She had virtually no idea who he was, other than that he was an alien from another world who saved people. The Doctor only once talked about his past, and never mentioned it again. Twilight wasn't sure if Derpy knew who the Doctor was.

"All you need to know, Spike, is that it doesn't matter anymore. The TARDIS is gone. I have no reason to stay in this town, now. But, because I have friends here, I'll stay around for a little! Oh, I'll need a name... 'John Smith' isn't really a name you hear around Ponyville very often... Oh! I got it! 'Time Turner'! Ha ha! It's better than 'Random Pony Who Travels Through Time' isn't it?" The Doctor continued on one of his annoying, yet charming, rants that no pony understood.

"Anyway..." The Doctor said, straightening his bow tie and clearing his throat. He took a quick look around the dark console room, and turned to his companions. "Let's see if we've moved, shall we?" He said with a grin.

The TARDIS doors opened with an audible creek, as the Doctor poked his brown head out from inside. He looked around to discover that that they are still in Ponyville, but have moved out of Twilight's library. They were in the center of town, no pony paid attention to the blue box that had appeared out of nowhere. Stranger things had happened in this town. Nightmare Moon, Discord, Heck, even the Hydra itself! Nothing scared these ponies anymore.

So no pony paid any attention to the strange blue box that had appeared with a loud noise.

The Doctor stepped out of the TARDIS, once again straightened his bow tie. "Blasted thing... Always coming out of place... Anyway! Ponyville! TARDIS! Something wrong! Investigate!" The Doctor said, giving a slight jolt and then continued through the town square. It was much like the rest of Ponyville, save for the town hall and a statue of Mayor Mare, thankfully no longer a Weeping Angel.

Twilight and Spike then came out of the TARDIS, followed by Derpy, who all looked around to find they were in the Ponyville they knew and loved. "TARDIS is dead... Can't go out and see the universe. I've been here far too long, possibly a day or two late... Wouldn't have worked if I tried to re-power it with my life force. My body has grown accustomed to this form... Stuck in this Universe forever. A Time Lord without access to Time. Like taking a Pumpkin out of its patch."

The Doctor closed his eyes, and sighed. "Well, come along, friends. We have some investigating to do."

Darkness...

The Doctor's ears pointed straight up in the air. He had heard a voice... a raspy, whisper.... "I-it's nothing... J-just... Time Lord jitters?..." He tried to assure himself.

One...

"!!" The Doctor took out his Sonic Screwdriver and pointed it directly at Spike, causing all of his companions to stagger back in shock. The Doctor then pointed the Screwdriver to Derpy, then Twilight.  "Augh!" The Doctor's body contorted, making him drop the Screwdriver and grunt in pain. His friends rushed to his side, Twilight picked up the Screwdriver and put it in the Doctor's collar. He may not wear a shirt, but he wears a tie.

Two...

"AUGH!!!! I need to get inside!!!" The Doctor screamed.  Twilight picked up the Time Lord and escorted her friends to the Library, the Doctor still screaming in pain.

Three...

The Doctor rested in Twilight's bed. He had a very high fever, and constantly had violent spasms of pain. When the Doctor was conscious, he had told them that he was not regenerating, but something was extremely wrong. If they did not resolve this quickly, then something would obviously go wrong. It is the way the Doctor's life was. Doctor is down, aliens invade. It is like the universe had something against him...