The Doctor was so close to losing everything. If the Master activated the tower before the Doctor could stop him, he would lose Octavia, his friends, his mind and he would never see his universe again. Everything was on the line and the fate of Equestria, and possibly the entire universe, was resting on his shoulders. This seemingly increased the speed at which he was running but the Master was still out of reach as he was always two hoofsteps ahead of him.

It was rather surreal that he was essentially chasing himself, or alternatively, he was chasing an old enemy in a new form. Some things never change, some foes never truly leave, and running would always be a necessity in his life. The chase through the winding corridors had taken a lot out of both beings, but the Master’s powerful pony legs propelled him forward. The Doctor soon realised that he wouldn’t be able to catch him at this rate, so his only hope would be to catch him on the ladder.

Previously when the Master had been called the Doctor, he had shown his counterpart the blueprint of the tower, and the Doctor had wondered why there was a second activation switch at the top. Now it was clear. When the Master placed his remaining regeneration energy in the top of the tower, he would immediately activate the device to ensure minimal complications. The Master was leading him right to the tower as the Doctor was beginning to fall behind. The Master had just slipped out of sight as they reached the final stretch to the roof.

The Doctor quickly found the spiral staircase and sprinted to the top. Only to find a locked door waiting for him at the top. This had bought the Master several valuable seconds as his counterpart had to unlock it with his sonic screwdriver. The Doctor threw the door open to find his counterpart already climbing the ladder. The Master spotted the Doctor across from him and took a moment to gloat.

“You’re too late Doctor! You can’t prevent the resurrection of my species. Soon the Time Lord’s will rule over this miserable universe and I will lead you all too prosperity!”

The Doctor had nothing to say as he bolted for the ladder while the Master continued to climb to the top.

Meanwhile…

“Hey everypony. I can move my hoof!” Vinyl’s sudden outburst lifted the spirits of everypony in the room. Almost instantaneously, the residents of the room began to feel the strength in their limbs return. Although it wasn’t enough to actually stand up again, it was a start. This development wasn’t enough to satisfy Rainbow Dash though.

“It doesn’t matter though. We need to actually stand up and get to the roof. The Doctor is up there with that psy-psyco-psyc…”

“Psychopath, dear,” finished Rarity.

“Yeah, that maniac. The point is our friend is up there all alone. I don’t care what he did, he ain’t a bad guy, I know that much.”

“I agree with you, Element of Loyalty,” announced Luna as she struggled to move. “It’s clear that he never set out to hurt anypony, and I believe he has done more good than harm. If anypony can save us now, then it is him.”

“Yes, well said Lulu,” agreed Celestia. “We must put our faith in him while we regain the ability to move. Only then can we worry about the consequences of what I’ve done.”

“You we’re mind controlled princess, nopony can blame you for what happened,” assured Fluttershy.

“You may be right Fluttershy, but I doubt it. I have no intention of abdicating; I know what chaos that alone would cause. But I doubt the papers will be kind to me after this.” Everypony struggled for a moment until Pinkie broke the short silence.

“You know what? I think the Doctor is going to be alright up there.”

“Did your Pinkie sense tell you that, Pinks?” asked Rainbow.

“Nah, it’s just a normal feeling in my stomach.”

“I hope you’re right Pinkie, I really do,” Octavia muttered under her breath as she continued to struggle to her hoofs.

Meanwhile…

The Doctor desperately clambered up the ladder as he realised the Master had nearly made it to the very top. The Doctor’s long limbs had played to his advantage on the ladder as he quickly closed the distance between himself and the Master, but he hadn’t reached the very top before the Master climbed over the edge.

The Master didn’t waste a second as he began to channel the energy inside of him and release it into a large dish located in the middle of the platform. The dish was meant to hold the cyber technology, when in reality, it’s purpose was to control the regeneration energy and keep it in one place long enough for the weapon to fire.

A golden aura suddenly shot through the Master’s body and fell straight into the dish through the his forelegs. The more energy parted from his body, the wider the Master’s grin grew till it became nothing more than psychotic. The Doctor had nearly reached him when the last of the energy build up had departed the Master’s body. The Time Lord practically leapt at the fire switch and pulled it downwards. Everything was finally coming together. The tower only needed several minutes to charge before it fired. There was nothing the Doctor could do to stop it.

Speak of the devil, the Doctor had finally reached the top, but the Master was one step ahead. He pulled out his sonic screwdriver and pointed it at the bolts that was keeping the ladder in place. The bolts began to unscrew themselves but just before they came off, the Doctor leapt from the ladder and grabbed onto the platforms edge. The ladder fell from the platform and landed on the roof with large CLANG. The Doctor barely held onto the platform with his fingertips. For a moment, he totally forgot about the Master until a brown hoof stomped on his left hand. A sharp pain coursed through his hand and the Doctor was forced to let it drop. The only thing preventing him from falling to the ground was his right hand, which was desperately holding onto the platform.

“Well what do we have here?” asked the Master in a mocking tone, “oh that’s right, a pathetic excuse for a time traveller. You had the nerve to call yourself the Doctor! I turned the meaning of that word from one of healing, to one of fear.” The Master was now standing over the Doctor. He looked down on him as he struggled to hold on. “Look at you, you could have joined me, but then you spat in my face! Morality has no place in the universe, years of running have shown me that. You’re too late now anyway. All my regeneration energy is in the dish and soon it will be combined with the raw magic to transform everypony within the Equestrian border into Time Lord’s that will follow my rule.” The Master raised his right hoof to stomp on the Doctor’s remaining hand. “And now, I have the pleasure of killing you. A fall from this height will kill you instantly with no time to regenerate. Goodbye, Doctor.”

The Doctor saw his chance. The Time Lord using the last of his strength threw up his left arm and grabbed onto the the Master’s raised leg. The Master, now afraid that he might be pulled over the edge by the Doctor was forced to pull back, but in the process, he accidently pulled his enemy safely over the edge. The Doctor had no time to recover as he dodged a buck from the Master. Instinctively, the Doctor pulled out his sonic screwdriver and pointed it at the Master. The Master did the same, pointing his at the Doctor.

“Stop the tower from firing, NOW!” Demanded the Doctor whose rage was released for the Master to see. The Master let out a small, dark chuckle.

“You are in no position to demand anything. Even if I wanted to stop this device, I cannot. Without the regeneration energy, only the raw magical energy would release which would become unstable and explode. Plus, there’s no shut off switch at this point. The energy will be released, hell, even if you were willing to sacrifice yourself, you can’t remove the regeneration energy from the dish.”

“I promise you one thing, I will stop you.”

“Another empty promise? How many companions have you promised you would come back for, only to never see it through? How many beings have you promised would survive, only to die? You’re promises are empty and worthless.”

“Not this one. I will stop you, even if I have to die as well.”

“Then let us battle, Doctor. You and me, fighting like this, for some reason, this feels right to me.”

With that, two ancient enemies charged at each other, ready for one last fight…

Meanwhile…

Spike’s eyes began to slowly open to the colourful world around him. He thought it was rather odd that he wasn’t in his usual bed. Instead, he was in the middle of Ponyville square. Despite sometimes trying to dodge a job or two, he never thought he was Rainbow Dash levels of lazy. So why he was trying to nap in the middle of the square was lost on him. Then he noticed the massive pile of metal objects beside him.

He sat up to get a closer look at the pile, only for his attention to be stolen by the fact that nearly everypony in town was lying on the floor, asleep. He could see Flitter and Cloudchaser helping each other up. Question Mark was by their side, checking if they were alright. Mayor Mare was starting to stand on shaky legs and several other ponies were just getting up as well. It seemed like everypony just decided to take a nap. Then he remembered everything.

They all met up for Mayor Mare’s announcement, only to lose all their senses. Every emotion, every bit of free will they had in them had suddenly vanished and the only impulse left in them was to follow orders. Whose orders though was somewhat of a mystery at this time. Spike turned his head several times to see if he could spot his friends, but he could only see Twilight and Applejack several hoofsteps away from him. The rest of his friends were nowhere in sight.

For a moment he panicked at the thought that Twilight might not wake up, but as he approached her, Twilight began to stir slightly, much to Spikes relief. He gently shook her to help rouse her and almost simultaneously, Applejack began to awaken as well. Twilight had the same thoughts that Spike had when he had woken up previously. Why was she napping in the middle of town square? Then, just like Spike, her memories of everything that had transpired came back to her. She immediately took the earpieces still in her ear and crushed them in one stomp.

“Oh my goodness, the Doctor was right. I don’t understand, why would the Princess do this?” The look on Applejack’s face indicated that she remembered as well. Spike put a reassuring claw on Twilight’s shoulder.

“Maybe the princess was being controlled as well?”

“Yep, I think Spike is right. I just can’t see the Princess doing sumthing like this willingly,” agreed Applejack who seemed to have regained all her senses.

“But who stopped this? Did the Princess break free?” questioned Twilight.

“Twi, I got this feeling that our flanks were saved by a certain Time Lord we know,” assured Applejack. Not another word was said as the three of them began to check on the other residents of Ponyville that were beginning to wake up.

Meanwhile…

Neither Doctor was a stranger to fighting, only increasing the amount of crap they were beating out of each other. Fists and hoofs went flying at the other in a desperate attempt to incapacitate their opponent. The Doctor needed to think of way to stop this and he couldn’t do that with the Master in the way. The Master, despite being certain of his victory, wanted a definite guarantee by getting rid of the only one who had a ghost of a chance at stopping him.

The Master in one swift buck landed a strong strike that caused the Doctor to fall to his knees. In his weakened position, the pony Time Lord landed another strike which sent the other Time Lord backwards as he nearly fell from the platforms edge. Despite being dazed, the Doctor noticed the Master sending another strike so he dodged it by rolling out of the way. The Master’s hoof only met steel. He yelped in pain while the Doctor quickly stood up and punt kicked the Master in his large chin.

The Master seemed out of it for a moment, so the the Doctor took advantage of this distraction and ran over to the dish. He needed to find a way of getting rid of the energy, but what? A buck to the Doctors’ knee caused the Time Lord to topple onto the ground. The Master had regained his senses and was now taking advantage of his opponents desire to stop him.

“I knew you’d run over here as soon as I was dizzy. It’s time to end this, Doctor!” However, the Masters rant had given the Doctor enough time to ram his sneaker into the Time Lord’s muzzle. The Master went flying backwards as his head hit a steel beam. Despite not being out cold, the Master appeared to be in too much pain to fight anymore and simply sat there with a smug grin on his face.

“It doesn’t matter! You can’t stop the tower from firing now. The energy is in place and all the tower has to do is charge up and release its energy across all of Equestria!” The Doctor took his eyes off his fallen opponent and turned to the pool of regeneration energy. The golden aura sparked and danced in place with no sign of leaving the tower just yet. “So close now!”

The Doctor willed his brain to come up with something, anything that would get rid of the regeneration energy. It didn’t matter if he died at this point, he just had to stop the tower from firing. He thought back to all his regenerations before, how he used the energy, how he expelled it from his body once, how he can… that was it! They may not be the same species, but they were similar enough that he might be able to absorb the energy. The Doctor stood over the dish and focused on the energy in front of him. It immediately started to draw near the Time Lord and enter inside his body. The Master could only watch on in horror as his plan began to fall apart.

“WHAT ARE YOU DOING!?” he cried out.

“Something wonderfully stupid, or stupidly wonderful,” the Doctor replied with an all too familiar smirk. The Doctor now had a golden glow around him, but before he could celebrate his victory, the tower fired which released raw magic, but with nothing to combine it with, there was an explosion.

If you were in Canterlot and you looked towards the palace roof you would see three things. A disturbing looking tower exploded and two lifeless forms falling from the top if the tower. One form, which looked like a pony, fell completely out of sight. The other, a humanoid figure, seemed to land back first on top of the roof.

Author's Notes:

To explain the Doctors, or rather Masters motivation is simple. It;s a twisted version of the Doctor's good nature. I was inspired by a Tom Baker episode where he encounters a future version of himself, who is evil. It annoyed me though, that he was completely different to the Doctor.

Basically, the Doctor is greatly disturbed after what he did in the ultimate war. The Timewar. In this reality, he never really recovered, so he came to the conclusion that to stop war, all would have to blindly follow one pony. And in his madness, he came to the conclusion that it would have to be him.

I hope that clears up a few things.

Next Chapter: Two Doctors?

https://www.youtube.com/watch?v=ceStLYpQxk8&list=FL1nAu47c9N_mOd00e3NIACg&index=2