The Doctor stormed through the ship, having traced the teleportation signal straight into the middle of it. The TARDIS had insisted he make a few stops first, and since it was a Time Machine he didn't really have an actual reason to hurry to Clara's location apart from worry. He trusted that the TARDIS had brought him to the right place and knew that Clara was close. He looked around, holding a pen and preparing to mark his arm if he saw any of the Silence but for some reason they seemed to be leaving him alone. His lip curled; maybe they were just too scared to face him.
He entered the next room and found himself in a huge chamber that looked suspiciously like a TARDIS control room. Then he recognised it as the same TARDIS control room he had encountered with Craig Owens and when Amy Pond had been kidnapped by the Silence while she was a ganger.
"This place again," he said looking around. Then he heard a muffled sound. He went around the consol and saw Clara, bound and gagged on the floor. She shook her head at him desperately making muffled noises through the cloth tied tightly over her mouth.
"Typical Doctor," said a voice and a blonde haired man stepped out behind Clara, "Always willing to dive headlong into peril to rescue one of your beloved companions." The Doctor stared at the man in disbelief.
"You died," he said, "How can you be here?" The man rolled his eyes.
"Oh please," he said, "You should know by now that I don't need regenerations to survive. How many times have I been resurrected; three? And they did not require regenerations."
"But how could you escape the Time War?" the Doctor said, "I saw you go into the Time Lock with Rassilon and the others. Gallifrey was only hours away from destruction. How could you possibly break out within a few hours?"
"With your pretty little companion," the Master replied and stroked Clara's long dark brown hair. She jerked her head away from him muttering something into her gag, "You've been wondering how she can be split through the Universe Doctor. Well I made her this way. And not only that, I also started the religious order of the Silence; the species insisted I name it after them. Of course finding you got much harder when you erased yourself from the Universe so I needed a sleeper agent to keep an eye on you."
"You started the Silence?" the Doctor gasped.
"Oh yes," said the Master, "And told them about the Question; I was the one who started the prophecy. Of course I already know the answer; you remember our childhood on Gallifrey just as well as I do I'm sure. If you'd known back then that we were going to become mortal enemies, I'm sure you would never have dared to tell me your name."
"Yes I've regretted that for my whole life," the Doctor admitted, "But you forgot it when Rassilon put the drumming in your head didn't you?"
"Yes well now that Gallifrey is truly destroyed, the drumming has stopped," the Master said, "After tormenting me ever since I was eight years old, it finally stopped when Gallifrey fell. For that I suppose I should be grateful, but the truth is I've been feeling a bit lonely without it. So I decided it was time to bring back an old lover." Clara shook her head frantically, her wide brown eyes pleading with the Doctor, "You can deny it my dear, but it happened. You just don't remember it because it was in another lifetime."
"You seduced her," the Doctor growled, "And then you split her through time and space. That was how you got out of the Time War wasn't it? You took her to Gallifrey before I closed the Time Lock and scattered her DNA through the Untempered Schism to give you a link between Gallifrey and the rest of the Universe. And that link was even smaller than the White Point Star Rassilon used; literally only a few cells from her body thrown through the Untempered Schism which landed and grew into Clara in several mothers womb's throughout the Universe. That's why you didn't drag the rest of the Time War out with you; it would have split apart just like Clara's DNA if it had followed you out of the Time Lock but you only needed to latch onto one piece of DNA."
"Very good Doctor," the Master crowed, "You always said I was 'hypnotic'. Well I used my obvious charm and good looks to get the very first version of her to fall in love with me." Clara glared up at the Master who simply gave her a charming smile which made the girl want to spit in his face. She would have done so if not for the gag tied over her mouth.
"That is low, even for you Master," the Doctor snarled, "Seducing an innocent girl and then mutilating her DNA and forcing her to suffer through the entire Time War so you could keep the link until the final day." Another thought occurred to him as he remembered the Master's condition the last time they met. "Are you still losing Life Force?"
"Not anymore," the Master said cheerfully, "Stole a Time Lady's regenerations just before leaving the Time War. I took them from your old friend Romana as a matter of fact, and that restored this body to full strength and gave me an extra supply of regeneration energy." The Doctor glared at him.
"You tried to steal my regenerations once," he muttered, remembering when he had encountered the Master shortly after his regeneration into his Eighth incarnation, "How could I not sense you?"
"You're getting old Doctor," the Master smirked, "Your senses aren't as strong as they used to be."
"I can still sense another full Time Lord," the Doctor growled.
"Well obviously you can't because I was able to hide from you," the Master said then shrugged, "I'm a good telepath Doctor; I was blocking my thoughts and until now I was in the parallel reality where the Silence had telepathic powers so they helped me cancel out your senses. Time was in flux when you wiped out their telepathic connections so I stayed in the alternate reality where you didn't destroy their ability. Once I came to this reality I realised what you'd done and promised the Silence I'd reverse it."
"What do you want this time Master?" the Doctor asked, "Why did you get your memory proof lackeys to kidnap Clara? Come to think of it, how can you even remember them without an eye drive?"
"Contact lenses that work just like an eye drive but without obscuring my vision," the Master replied, pointing to his eyes; the contact lenses were only visible if one looked very closely, "Eye drives are easier to make but I prefer to be able to see through both eyes instead of just one, so I invented the lenses as an alternative means of remembering them. As for why I ordered my servants to kidnap Clara, the answer is I want you to reveal your true name."
"You know I can't do that," the Doctor replied.
"You can," the Master said, "and you will. You see Doctor, Rassilon may have been mad but he was onto something when he suggested the Final Sanction. I simply modified his idea a bit; I intend to open the Time War, with your name acting as the key of course, and that will tear the Time Vortex apart. But then I will use your TARDIS and the Pandorica to restore the Universe. It's a risk admittedly but when it works, I will have saved the Universe and everyone will worship me."
"So that's it," the Doctor said, "Just another Universal domination plan. You make me sick Master."
"I know," the Master said delightedly.
"You already know my name," the Doctor said, "Like you said before I told it to you when I was a child."
"Yes but the Time Lock is voice activated as you damn well know," the Master rolled his eyes "Only you can open it by saying your name."
"Master," said one of the Silent's, "We have arrived."
"Excellent," the Master said, "I'm sure you heard the prophecy of the fall of the Eleventh, Doctor. Well this is where it takes place. This is also the home world of the Silence before I took them to Earth. Welcome to the Fields of Trenzalore!"