Disclaimer: Doctor Who belongs to the BBC. I do not own any of it, nor do I get paid for it.

A/N Thanks for the awesome welcome back. I have finally got this story back on schedule. I have finals coming up but I am going to try and update regularly.

Anyway, here is the final part of 'The Clone Wars'. The Doctor, Amy and Rose launch a rescue to save Rory from the Vardans. Some past information, especially from 'The Invasion of Time'. Seriously, one of the best DW stories ever.

Happy Reading!

The Clone Wars: Mind Games

Previously

Over on the Vardan ship, Rory's eyes snapped open and he realised just how many scanners he was attached to. He looked up and saw several of the silver papery figures rustling and muttering amongst themselves.

He had to strain his ears to hear some of the words but he finally understood the gist of what they were saying.

"The Doctor has killed one of the Vardans we sent in as an impostor for the human male."

"He has threatened to attack."

"Prepare our defences."

"Put the human male in stasis."

"The Doctor must not be allowed to defeat the Vardans again."

"This time we shall be avenged."

"What…" Amy was staring at the empty space where Rory had been, with a bewildered look on her face. "What happened?" she asked in a low voice.

"It wasn't Rory," said the Doctor gently, patting her shoulder.

"No," said Amy, shaking her head. "I was talking to him. It was him…it had to be him."

The Doctor tilted her chin up and met her eyes. "The Vardans had connected their scanners to Rory's brain which was why they could replicate his reactions," he explained. "Amy, we will find Rory."

"Who are these Vardans anyway?" Rose asked, rubbing Amy's shoulder in comfort.

"They are telepathic beings," said the Doctor with a grimace. "They can travel on whichever wavelength they want but they generally prefer the silver waveform that we saw just now."

"And they have Rory? Since when?" asked Rose.

"Up on the plateau when we were being fired at," Amy realised. "I lost sight of him in the chaos and he came out of nowhere and grabbed my arm."

"They must have taken him and replaced him with a double," nodded the Doctor. "Good news is, he is alive."

"What's the bad news?" asked Rose, with a growing sense of dread.

"I can't remember how to fight Vardans," admitted the Doctor. "That part of my memory is suspiciously blank."

"Can you get an accurate reading on the thought patterns of the Doctor and his companions?"

"No, the catacombs have lead deposits. It is making it harder to use telepathy on them."

"What about the male?"

"He has been put in stasis."

"Good, then we shall wait."

"Wait?"

"The Doctor will be bound by honour to come in search of his companions."

"Bait and trap. Excellent."

"Is it safe to do this here?" Rose asked as they sat down in the clearing further down the passageway. It was a cramped space and did not give them much of a chance to move. When all three of them were sitting down, their knees were bumping with each other's.

"The Vardans faltered only when Rory walked into this passageway with us," said the Doctor briskly. He was now wearing his coat over his bare torso and the bandages were almost white. "There must be something about this place that disturbs the Vardans' telepathy. We can use this to our advantage."

"What exactly are we doing?" asked Amy, fidgeting impatiently. "Shouldn't we be marching into the Vardan ship and demand them to release him?"

"Without knowing anything about them?" asked the Doctor dryly. "You know better, Amy."

Amy gave a grudging nod. "Fine, explain it again," she conceded.

"Recalling suppressed memories can be a tricky process," said the Doctor. "Especially in this regeneration of mine."

"Why?" asked Amy.

"He's more telepathic in this one," explained Rose.

"Yes," nodded the Doctor. "Also, I have had a lot of trouble with my memory in this body. Not to mention the incident with the trap in the Eye of Harmony." Amy opened her mouth, probably to ask about the Eye of Harmony when Rose beat her to it.

"I got to meet all 7 of the Doctors before him," she said and then turned to the Doctor. "How are Amy and I supposed to help?"

"You two are going to enter my mind," he said in a grave tone. "Understand very clearly that this is very dangerous. I would not hold it against you if you don't want to."

"Just tell us what to do, Doc," snapped Amy as Rose gave a determined nod.

The Doctor looked at both of them and then nodded. "Once you are in my mind, you are going to help me open the doors of the suppressed memory. The reason that I can't do it on my own is that my mind will reject my efforts."

"So we are going to be your encouragement?" asked Amy. She understood telepathy a bit better since humans had started dabbling in mind arts by her time.

"Good way of putting it," said the Doctor with a small smile. "Yes, you two are going to encourage me to open that door. I will resist and rebel but you have to make me open it. Understand?"

Amy and Rose nodded in determination and the Doctor placed one hand against Rose's temple and the other against Amy's. "Follow the orange light," he said, gently guiding them into his mind.

The two of them did as he told them and slowly, they could see themselves walking down a dark corridor until they came to a door through the orange haze. It was a heavily guarded door with locks of all shapes and forms on it.

They exchanged a quick look before Rose thought. Open up, Doctor. It's us.

For a moment, it seemed like nothing had happened but then the elaborate door melted away, leaving a plain white door in its place. Amy pushed it open and the two girls were almost startled out of the contact due to the loud voices permeating the air.

One day, I shall come back. Yes, I shall come back. Until then, there must be no regrets, no tears, no anxiety. Just go forward in your beliefs and prove to me that I am not mistaken in mine…

You can't rewrite history. Not one line.

Perhaps I should go back. Back to my own planet.

There are some corners of the universe which have bred the most terrible things. Things which act against everything that we believe in. They must be fought.

People spend all their time making nice things and then other people come along and break them.

Free will is not an illusion after all.

Courage isn't just a matter of not being frightened, you know. It's being afraid and doing what you have to do anyway.

A straight line may be the shortest distance between two points, but it is by no means the most interesting.

Homo sapiens. What an inventive, invincible species.

Do I have the right? Simply touch one wire against the other, and it's it? The Daleks cease to exist?

The very powerful and the very stupid have one thing in common. They don't alter their views to fit the facts. They alter the facts to fit their views.

"We have to keep moving," hissed Rose as she heard the Fourth Doctor's voice. It seemed like they were getting snatches of conversations from the different Doctors and they had to go on before they got lost in the chatter.

Amy was fascinated. She had known about regeneration and that the Doctor had regenerated several times but to hear four different voices with the same man's wisdom was an astonishing experience. She would have loved to stay and listen to the Doctors who came after that but Rose was right. They had to get this done.

"This way," said Amy, pointing to the orange haze which was moving in a labyrinth closer to the Fourth Doctor's voice.

Amy and Rose followed the haze and they came upon a door that was locked tighter than the first heavily guarded door. This door looked impenetrable.

"Doctor, you have to open the door," said Rose. The orange haze darkened to a red but nothing happened. "Please, Doctor."

"No…" came a disembodied voice that sounded like an echo of all the Doctors, future and past, refusing.

Amy knocked on the door. "Doc, you gotta open up," she said. "Rory will die if we don't save him."

The red lightened to an amber but the door still wouldn't open. Rose patted the door, willing with all her might that he would listen. "Doctor, please, we have to know what happened. We have to know if there is a way to defeat the Vardans…we have to…."

"Rose," interrupted Amy, pointing to the door which was turning into a white door. As it became clearer, they saw a figure eight signet on the door.

"The Seal of Rassilon," said Rose and then opened the door.

A rush of sound and images floated through the door, too fast for Amy and Rose to register though they did catch words like Gallifrey, Leela, Andred, Borusa, Rassilon, Vardans and Sontarans. And suddenly, they were back in that narrow passageway on Maxim Beta.

"Doctor, are you okay?" Rose asked, as she saw the Doctor clutching his head.

"Yes," he answered and looked up slowly. "I know what we have to do."

"It has been quite a while. Perhaps the Doctor has given up any hopes of saving the human male."

"DO NOT underestimate him. We underestimated him once and were nearly destroyed by the time loop that he caught us in."

"Understood. We will continue scanning."

It was silent for a few moments as the Vardans continued to scan the asteroid for telepathic waves.

"We are receiving brain waves compatible with the physiology of the Time Lords."

"Excellent. He has taken the bait."

"Correction. The waves are getting weaker. He is heading towards his craft."

"He has decided to abandon the male? No matter. We shall follow him into his time capsule. Get rid of the human male."

"Oh hello," came a cheerful voice and the Vardans were nearly shocked out of their telepathic waves as the Doctor smiled at them. Somehow, he had got past their ship's defences and into the main control room without anyone noticing.

"Impossible," hissed the Chief Vardan.

"His brain waves still show their presence near his craft," butted in another Vardan with shock.

"Really?" asked the Doctor in mock-confusion. "My mind must have got away from me then." He laughed at his own joke, pretending not to notice the hostile looks he was receiving.

"You betrayed us, Doctor," snarled the Chief Vardan. "The insult must be avenged."

"Yes, I understand," said the Doctor, pacing leisurely in the control room of the Vardan ship. "But you see, until a few minutes ago, I had no memory of what I had done to warrant your anger. And I have to say, now that I know, it makes no difference. You wished to use me as a puppet to rule Gallifrey and you were thwarted. Betrayed by the Sontarans too, as I recall."

"The Sontarans have been destroyed," said the Chief sounding a tad smug. "Undoubtedly they will grow their clones again but they have suffered a setback. Our grievance is with you, Doctor. Now, you will die."

"Now?" asked Rose, tossing the newly revealed fourth segment of the Key between her hands.

"Not yet," said Amy as they watched the scanner. "They bought the ruse, didn't they?"

"Yeah," said Rose, tossing the segment aside, before picking up the contraption that they had used to mislead the Vardans. Their recent jaunt in the Doctor's mind had left them both with a slight headache and the Doctor had given them a device to magnify the residual brain waves resembling his, which would trick the Vardans into thinking the Doctor was in the TARDIS while he snuck onto their ship.

"He has to give the signal soon," said Amy, her hand poised over the lever that the Doctor had told them about.

"He won't give the signal if he doesn't see Rory," said Rose, biting her thumb in worry. "How long do we wait?"

Amy met her eyes. "As long as it takes?"

Rose nodded back determinedly. "As long as it takes."

Over on the Vardan ship, the Doctor was being strapped onto a flat surface. Rory was lying on a similar thing next to him but he appeared to be unconscious. The Doctor strongly suspected that he had been put in a stasis state.

"Before we end your life, Time Lord, all your secrets shall be ours," declared the Chief.

"Fine," said the Doctor dryly. "Just make sure you are prepared for them. Because I must warn you, my mind isn't the easiest place to be. Over a thousand years' worth of memories, you understand. Every life I took, every suffering I ever witnessed, every planet I saw die, every star I saw perish, every civilisation I saw fall, every friend I ever lost, every moment of pain I felt…EVERY. SINGLE. MOMENT. All of it. Up until this very moment. Right until NOW!"

Over on the TARDIS, Amy heard the word 'now' and pulled the lever. The sonic screwdriver in the Doctor's coat pocket lit up and emitted a sonic wave so high that it was nearly impossible to hear. But for every Vardan, it was the agony of the worst kind. Brain waves could be modulated and scrambled with a proper beam and conductor. The beam came from the TARDIS and the screwdriver was the conductor as the sonic wave pulsed through the air, scrambling the telepathic nerves of the Vardans.

They dematerialised slowly, screaming in agony the whole time. It was all over rather quickly yet the screams continued to echo for a while in the silence. The Doctor felt heaviness in his hearts at the murder he had just committed and he stayed unmoving until Rose and Amy ran into the Vardan ship.

"Doctor!" Rose ran to him as Amy set about removing Rory from the stasis state. "Thank god," she murmured as she got him free and threw her arms around him.

The Doctor hugged her back, grateful for her presence. He knew that he didn't have a choice. The Vardans were dangerous, even to Time Lords. It was his duty to stop them; he had done his duty, yet he felt pain at having to end the lives of such an intelligent species. There were undoubtedly more Vardans on their planet, perhaps still trapped in the time loop from years ago. The few that had been here had to have escaped from it in the first place.

He felt Rose kiss his forehead before hugging him tightly again and he felt the guilt begin to loosen. He pressed his lips against her hair, and realised that he would forgive himself in time. For now, her forgiveness was enough.

Rory felt like he had the worst hangover in years when he woke up strapped to a cold table. He spotted a flash of red and smiled. "Amy…"

"Hey," she said and his gaze focused to find her smiling face. "I'll get you down in a minute."

He nodded and tried to make the world stop spinning. He felt the restraints loosen and he nearly lost his balance but Amy grasped his arms, steadying him. "Hi," he said, opening his eyes and feeling the world almost tilt.

Instead of answering, Amy kissed both of his cheeks twice before hugging him tightly. Rory was frozen at the actions and when Amy released him, he stared at her with wide eyes. "Can you tell me what I did?" he asked her finally. "For future reference?"

Amy laughed and it looked like she was about to kiss him when the Vardan ship gave a lurch. Next to them, the Doctor and Rose snapped out of their embrace. "The sonic wave," the Doctor realised. "It has upset the planet next doors I think."

Rose looked at him with a wide smile. "Run?" she asked cheekily.

The Doctor laughed and met Amy and Rory's eyes. "Run," he agreed.

And so they all did. All the way back to the TARDIS.

A/N End of story #4 'The Clone Wars'. Thanks for reading.

So, what did you think? Grim ending I thought, but the Vardans had it coming. Very annoying aliens.

The next story is called 'Terror on Marquessa' and it will also feature an old enemy of the Doctor's. The next few stories are the ones that I am looking forward to the most. They will probably be my favourites.

Part 1 will be up soon. See you then! Let me know what you thought of this one.

~ Phoenix