Disclaimer: I don't own the Doctor, the TARDIS, Fitz, Trix, K9, the Vore, Daleks, Madame Xing (From 'Halflife') or the Nestene Consciousness; they're all the BBC. I just own this plot.
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AN: If you haven't read the Dr Who books, here's a basic summary. Essentially, the Doctor's history was altered and his third incarnation regenerated ahead of schedule, causing him to be infected with a virus that would turn him into a member of Faction Paradox, a cult of time-travelling voodooist that worshiped time paradoxes, which was only cancelled out by the TARDIS holding the new and original timeline within itself. In a desperate last effort, the Doctor triggered the TARDIS to be deprived of all its energies, destroying Gallifrey AND Faction Paradox, before wiping his memories to store the contents of the Time Lord Matrix within his subconscious. He was eventually reminded of the accident by one of the few other surviving Time Lords at the end of 'The Gallifrey Chronicles' by Lance Parkin, but then had to deal with an invasion of Earth by the Vore (See below). When the novel ended, the Doctor had just dived into their mountain base with his companions, Fitz Krienier and Trix MacMillan, with a plan for stopping them…
Filling in the Blanks
Standing back from the mountain, the Doctor and his companions watched, the Doctor with a small smile on his face, as the Vore mountain began to collapse in on itself before vanishing into thin air.
"Wow…" Ftiz commented, from where he was standing on the Doctor's right, watching the mountain vanish. He stared curiously at the Doctor. "Could you just explain again exactly how did you do that?"
"Oh, it was simple enough," the Doctor said casually, as though defeating a race of superintelligent bugs with a command of hyperspace systems was an everyday occurrence. "I just worked out that, like hummingbirds and bees flying through the air by creating a vibratory pattern by flapping their wings, the Vore's hyperspace tunnels could be activated by them by triggering a certain frequency. All I had to do once I got in there was figure out that frequency, trigger it using the sonic screwdriver, and then sent every single Vore remaining straight to-"
"Actually," Trix cut in, looking curiously at the Doctor at that last statement, "you never told us that part; where did you send them again?"
"The heart of the Sun," the Doctor said dismissively. "I wanted something large and nearby, and it fitted the bill exactly."
Here he smiled and looked back at Ftiz. "From there, it was easy; we just evacuated the mountain and I called General Lethbridge-Stewart and had him order a bombing raid on the mountain."
"And that's it?" Fitz asked, looking at his old friend.
Looking back at Fitz, the Doctor knew what his friend meant. He almost considered it ironic; ever since he'd woken up in that railway carriage in 1888, with no memories and only the small box that would grow to become the TARDIS in his pocket, he'd spent most of his remembered life waiting for Fitz; admittedly, he'd spent some time without him before, when Fitz had travelled to Siberia, but event hen, a part of him had known that Fitz would be back.
He nodded at Fitz, a nod of acceptance and resignation that confirmed his willingness to end their time together at last better than anything he could have said.
"That's it," he said, looking at his two old friends. They'd barely known each other a year- for him, that seemed such a short time, even without all his memories- and now, here they were, ready to leave him and the TARDIS and begin a new life, all of their own.
He looked at them both once again. "Are you sure you'll be all right?" he asked them, a slight note of concern in his voice. He knew that they could cope with the lives they'd chosen travelling with him, of course, but it wasn't the same as trying to live a permanent life on a single planet…
In reply, Fitz and Trix put their arms around each other's shoulders, and Trix smiled up at the Doctor.
"We'll be fine," she reassured him. Then a thought occurred to her, and she looked back at him. "But what about you? I mean, after… well, after all that…"
"Oh, don't worry about me," the Doctor smiled. Then he cocked his head to one side in an almost quizzical manner, as though hearing something off to one side…
"What?" Fitz asked, noting the change in the Doctor.
"Oh, nothing," the Doctor said, turning around and heading off behind a nearby tree. When he came out from behind it, he was being followed by…
Trix blinked in surprise.
"A robot dog?" she asked, looking up quizzically at the Doctor.
"Affirmative," the dog said, looking up at her with its single red eye, somehow managing to look smug without any actual expression on its face. "I am K-9."
"Oh," Fitz said, looking back up at the Doctor while Trix continued to stare down at K-9. "And K-9 is…?"
"Oh, many things," the Doctor replied, smiling. "An old friend of mine, something I whipped up in my spare time, a useful means of defence and finding information, but, more importantly, you may consider him my housewarming gift for the two of you."
Trix looked up in surprise.
"What!" she said, staring at the Doctor.
The Doctor shrugged. "Well, I can hardly keep a dog with my lifestyle, can I?" he asked, smiling pleasantly at them. "Besides, I'd like to ensure you have someone to keep an eye on you two, and K-9 seems like the best candidate for the job. Right, K-9?"
"Affirmative, Doctor-Master," K-9 said, nodding its head slightly at the Doctor. Then it looked back up at him, again somehow managing to appear curious despite its lack of any real features on its face. "Is what I have acquired satisfactory?"
"Oh yes," the Doctor said, nodding at K-9. "Trust me, it'll be fine."
"What?" Fitz asked, looking up at the Doctor. "What did he get you?"
"Oh, just a little something from an old friend," the Doctor replied casually. Then he turned around and began to walk back towards the forest where he'd moved the TARDIS; the three of them had been forced to evacuate the Vore mountain by a route that unfortunately didn't leave them particularly close to the TARDIS.
"Wait!" Fitz called after the Doctor, who turned around to look at his friends one last time.
"Yes?" he asked.
Fitz didn't reply. Instead, he walked up to the Doctor, and, solemnly, held out one hand.
The Doctor shook it, looking Fitz in the eyes as he did so.
"Thanks," Fitz said simply as he looked at his old friend. "For everything… Even the bits you don't remember. I… well, I wouldn't be who I am today if it wasn't for you"
The Doctor nodded in reply. "I'm glad I could help," he said. He looked back at Trix and K-9, and smiled slightly at Fitz. "Take care of them."
Fitz nodded. "Take care of yourself," he said.
The Doctor nodded back, and then he turned around and continued to walk towards the forest, heading back towards his TARDIS and out of their lives for good.
For a few seconds, Fitz watched his old friend's bottle-green-and-cream-clad form fade gradually away, his longish brown hair blowing slightly around his head in the wind. Then he sighed, smiled, and turned back to Trix and K-9.
Now all they had to do was wait for a plane to pick them up after checking the mountain for Vore survivors- that UNIT group had mentioned they'd send someone along to pick them up after hearing about the Doctor's presence, and there was still Rachel to recover, even without them-, and they were set.
Their time with the Doctor was over.
Now it was time to start living the life the Doctor never could, and wish their old friend luck in returning to the life he'd once had and regaining the memories he'd once possessed.
Stepping back into the TARDIS, the Doctor closed the door behind him and studied the surrounding console room. He'd grown attached to the old thing over the years, but he had to admit that this new design it was creating after that cold fusion explosion had its positive sides as well; larger, smoother lines and remaining equally spacious, with large winding pillars that almost resembled the smooth bones of living creatures around its edges. The metal grating that acted as the floor managed to compliment the almost organic surroundings rather than clash with them, and the control console in the centre, with the Time Rotor sticking out of it, continued to make him feel better every time he saw it.
Reaching out with one had, he stroked the glass softly, smiling as he did so.
"We've had some times, haven't we, old thing?" he said to it. Then he looked up at the ceiling. "Didn't we have another of you in here somewhere? I need some storage space for… things"
In answer, a long stream of lights lit up along one wall, running along towards the door that led deeper into the TARDIS. Curious, the Doctor went through the door and followed the illuminated roundels in the wall, until, finally, he arrived in a smaller room, white, with a six-sided central control console.
Reaching out, the Doctor patted it affectionately.
"Hello there," he said casually, not caring that it might be taken as an odd thing to do by anyone else. "It's been a long time, hasn't it?"
The TARDIS console didn't reply vocally, but a brief blinking of lights seemed to indicate it was glad to see him again.
The Doctor stood there for a few seconds. Then he reached into his pocket and pulled out a fairly large black box-like device with two handprints in one side. He placed it on the TARDIS console, near two circular objects, and then placed his hands upon it.
This box was what K-9 had collected for him; a modified viroid from the planet Espero, developed by a mysterious woman called Madam Xing. Under normal conditions, the viroid allowed the user to regain memories that may have been lost due to some accident or trauma, but, on the Doctor's request, this version had been modified to serve another purpose.
Namely, to boost the circuitry of this TARDIS console to allow him to store the contents of the Matrix within the TARDIS.
It wasn't much of an option, he'd admit, but, now that he knew what it was he'd done, the Doctor found himself wanting to know the rest of the fine details about his past. His family, his old friends, his old enemies…
And the only way he'd ever learn that was if he gave the Matrix a new home to protect it when he restored his old memories.
Reaching down, he grasped the viroid with both hands, and focused inward, searching for the contents of the Matrix in his mind, underneath all his new memories formed since the accident.
He touched them. All the memories of every single dead Time Lord that ever was, all kept in his head, waiting for this moment…
For a brief moment, there was nothing.
Then, the Doctor opened his eyes, and the faint voices were gone.
He was alone in his head once more; even when he hadn't known about them, there'd still been a nagging 'presence' in the back of his mind, but now that was gone, leaving his inner head silent once again.
He looked at the console for a few seconds. Then he reached into his pocket and pulled out another, more conventional viroid.
He looked at it, and sighed briefly, expelling the last of his doubts as he looked resolutely at the object in his hands.
The time had come.