Author's Note: New story. Yesterday was Jon Pertwee's birthday and he would have been 95 if he was still with us. Since he was the Doctor who really drew me into the show when I was casually seeing it on and off, I wanted to write something for the 3rd Doctor even though it would be posted a day late. Plus, I've wanted to try my hand at writing the 3rd Doctor and the Brigadier for a while now, thus this one-shot was born. I hope my readers like it. :)

Time-line wise, this takes place at the end of Season Seven after Inferno and before Terror of the Autons at the beginning of Season Eight.

I do not own Doctor Who or any of its characters.

Thank you to everyone who reads/favorites/reviews this. It is always appreciated. :)

What Lies Hidden

It was an unusually quiet atmosphere at UNIT headquarters that evening. There had been no reports of unusual activity anywhere in England for the last few days and nothing outlandish happened elsewhere to warrant serious investigation. As a result, many of the soldiers had taken the night off with only a few of them remaining for basic tasks like guard duty or tackling the mountain of paperwork that never seemed to decrease.

Tucked away in an isolated corner of the UNIT complex was a large laboratory that overlooked the water. Normally, UNIT laboratories were staffed by several scientists who worked together on a limited range of projects and experiments. However, this laboratory was unlike any of the others. The fact that there was an old-style police telephone box in a corner of the room was only the beginning of those differences.

Even though almost all of the other scientists had long since gone home for the evening, the Doctor, who was the sole scientist who used this laboratory, was still there and still working. The room was mostly silent other than a few moments when the Doctor broke out into song while he worked.

Currently, he was sitting at his work table, gingerly manipulating a needle-thin instrument against a circuit board from his TARDIS. For the past couple of days, he suffered through the tedium of consulting the TARDIS' operation manual to re-familiarize himself with the purpose of these circuits and to gain some insight into how he might be able to manipulate them to regain control. There had been more than one frustrating dead end in his research due to the Time Lords 'adjustment' of his memories, but the Doctor was confident that he was making progress.

The Doctor grimaced and leaned in closer to the circuits in front of him. It had taken plenty of pestering to convince the Brigadier that the supplies needed to alter these circuits were a necessary expense for UNIT. There were times when the Doctor worried that the Brigadier would eventually put his foot down and declare a halt to his continuous demands for equipment, but so far the soldier appeared to be willing to honor his requests without too many questions.

A few more adjustments later, and the Doctor was certain that it was time for a test. He carried the circuit board back into the TARDIS and installed it into the base of the central column in the console room. He paused for a moment, checking his recently learned memory, before flicking a pair of switches and waiting for the results.

They were not long in coming. A high pitched whine erupted from the column and sparks spat out from the dials near his hand. He jerked his hand away, but not fast enough to prevent the side of his palm from getting a slight burn. The Doctor turned the switches back and yanked the circuit board he had just installed out of the console and threw it to the floor, the device now singed and black.

"Blast! Another month of work, wasted!" the Doctor snarled. He bent down to pick up the circuit board and strolled out of the TARDIS just to gain the satisfaction of throwing it again, this time into the waste bin. He glowered at it for a couple of moments before running his hands down his face and moving to stand by the window.

By this point, the moon had risen and the dim light of stars was coming into view. These days, the Doctor frequently avoided looking at the night sky, the stars above him a poignant reminder of what he had lost when he had been exiled to Earth. But for some reason, tonight he couldn't stop looking at them.

The Doctor scowled again. He was determined to not give up on his quest to repair the TARDIS and regain his ability to pilot it, but he couldn't deny that it was a wearying struggle. Trying to retrieve the memories he was searching for was like trying to grasp water in his hands: he could always clutch at them for a moment, but they ran through his fingers in so little time. The fact that his memory had been modified in the first place was a constant source of frustration and anger to him, and he groused about it often.

However, it was during moments of calm like this the Doctor found himself confronting the truth that the loss of his memories also chilled him to the marrow of his being. To think that he might have lost parts of who he was and all that he had gained since leaving Gallifrey was an unbearable idea to contemplate for any real length of time.

"Och, Doctor, don' worry. Ye're still the same clever, daft man ye always were."

A sad smile appeared on the Doctor's lips. Even though Jamie wasn't physically present, his spirit never seemed too far away. Still, that did not mean that the Doctor had stopped wishing that the stalwart piper was here with him now. Jamie had always been an expert at keeping his morale up when things were at their worst, despite the Scot's own tendency to be quite the pessimist himself.

The Doctor glanced back at the empty laboratory and shook his head. Two weeks ago, Liz had informed him that she was leaving UNIT and would be going back to Cambridge to continue her own research. The Doctor wished her well and was secretly sorry to see her go, but had found it impossible not to sympathize with her reasons. Working for UNIT came with a lot of restrictions, many of which actually got in the way of real scientific progress. Besides that, as much as Liz seemed to be intrigued with the knowledge he had to offer, it was clear that she was more interested in figuring things out for herself rather than having him instruct her about the concepts and technology he was thoroughly versed in.

However, even though he had understood the reasons why Liz left and agreed that it was probably for the best, it had reminded him of how he was alone, trapped on an alien world with no one around him who he could rely on or trust. It was then that he felt the losses of Jamie and Zoe keenly for he strongly doubted that he would be able to find anyone here at UNIT that he could bond with in any meaningful way.

'Narrow, regimented minds,' he silently fumed. 'They have no interest in learning, in discovering new things or in reaching out to other species. They're all completely wedded to their militaristic outlook. "If a problem gets in the way, blow it up." That's their mindset.'

The scowl on the Doctor's face deepened. Every once in a while he still thought about the Silurians and about all the tragedies surrounding their conflict with humans that could have been averted. It had been a pointless waste of life on both sides. Even worse, the Brigadier's decision to act so callously and with such prejudice had been a severe blow to the Doctor's certainty that he could count on him as a potential ally.

"Working late again, Doctor?"

The Doctor whirled around to see the Brigadier standing in the doorway to his laboratory, the baton he usually carried tucked under his arm, and a tray of glasses and a bottle in his hands.

"Yes," the Doctor said, walking back toward his work table. "And I would like to get back to it as soon as possible, so unless you have something important to discuss with me…."

"Nothing official, no," the Brigadier said as he walked into the room. "But I feel that it is important just the same."

"All right," the Doctor said, sitting down on a nearby stool. "What is it then?"

The Brigadier did not respond right away. Instead he sat the tray onto the table along with his baton. Then, he poured a dark liquid into a pair of glasses and placed one in front of the Doctor and put one by his own elbow.

"I think it's time we had a serious conversation about your position here at UNIT," the Brigadier said as he sat down across from him.

"A conversation that requires scotch?" the Doctor said, nodding at the glasses.

"I find that a shared drink makes it easier to be frank," the Brigadier replied. "Do try it. It was a gift from an old friend of mine when he made colonel. It's some of the finest I've sampled in many years."

"Thank you," the Doctor said, still not touching his glass. "But hadn't you better tell me what this is about?"

The Brigadier eyed him for a moment before taking a long sip from his glass. Once he was done, he sat it down and leaned forward.

"Doctor, if you are going to act as UNIT's scientific advisor, we need to reach an understanding," he said.

"I thought we already had," the Doctor replied. "You supply me with a place to live and work and I assist you with the problems beyond your planet's comprehension."

"That was our agreement, yes," the Brigadier said. "But over the past few months, it's become painfully clear that your position of forced compliance will not be beneficial to my organization in the long run. Doctor, if we are to work together, we will need to find a way to be on the same page at least some of the time."

"Brigadier, I honestly don't see how that will be possible," the Doctor said, frowning. "You and your organization's goals are usually at odds with mine."

"In what way?" the Brigadier asked. "When I first met you, you seemed to be sufficiently invested in protecting Earth from alien threats, the same as I."

"Not at the expense of an entire species," the Doctor snapped. "A species who had just as much right to exist as yours."

"I thought that that might come up," the Brigadier grimaced. "Whatever you think of my decision in regards to the Silurians, Doctor…."

"Very little, I can assure you," the Doctor interrupted.

"Whatever you may think of it," the Brigadier continued, undeterred. "The fact remained that I was facing a very real threat to the safety of our people and you had not presented very much in the way of proof that you would be able to find a solution that did not involve a vast amount of unnecessary risk."

"And that's how you saw it, was it?" the Doctor retorted. "As nothing more than a threat to your precious security and a risk that that you couldn't bear to take. I suppose that was easier than viewing it as an act of genocide which it was."

"That's where you're wrong, Doctor," the Brigadier said. "I'm fully aware of the consequences of my actions, despite your assertions to the contrary. But that does not change the fact that I had a responsibility to defend this country and this planet, a responsibility I take very seriously. You may have been able to view the situation purely on the basis of your personal morals, but I do not share in that luxury. My decisions cost lives, and for me, it's a matter of making the decisions that have the best chance of mitigating those losses as much as possible."

The Doctor frowned again, but remained silent. Despite his firm belief that the Brigadier had made the wrong call, he could appreciate the fact that the solider had tried his best to save lives rather than squander them. He had met far too many military types in the past who were far too willing to sacrifice the men under their command for the flimsiest of ideals.

He thought back to the conflict they had faced against the Great Intelligence in the Underground, and how distraught the Brigadier had been when he lost almost his entire troop in a failed attempt to get to the TARDIS. It had been a rare moment of fragility on the Brigadier's part, and it told the Doctor volumes about the type of commander he was at the core.

The Brigadier took another swallow of his drink and held the glass close to his lips for a few seconds before moving it away.

"What I don't understand, Doctor, is why you find it so difficult to work with me now?" he continued. "Back when you were…well, when you were different, you seemed to be willing to see eye-to-eye with me. It's as if you've become someone else now."

"You still don't believe that I am the Doctor?" the Doctor said, narrowing his eyes slightly.

"I didn't say that," the Brigadier answered. "No, I accept that you are who you say you are. For now anyway. But you still did not answer my question. May I ask what exactly has changed? Apart from the obvious that is."

The Doctor crossed his arms over his chest. A part of him wanted to blurt out the truth: that he was disgusted with his previous self's judgment and that he wouldn't be the least surprised if that incarnation had also been wrong to trust the Brigadier. But as angry as he was at his former self, the Doctor was also aware that it was unfair to the Brigadier to view him through the lens of that frustration.

'But is that the only thing that is making me hesitant?' he asked himself. 'Perhaps I'm letting…other recent events color my perception.'

The Doctor let his arms fall to his sides as he relaxed his posture. If he was honest with himself, he would have to admit that a part of him had still not shaken the memory of the Brigadier as he existed on that parallel world he had recently visited. Petty, cruel, and violent: that Brigadier had been all the things the Doctor sometimes feared was lurking below the surface within the Brigadier he knew in this world. It had been easy for him to seek the potential for good within Liz in that world, but he had made no similar attempt with the Brigadier. As he reflected on it now, he realized that it had been nearly effortless for him to connect these two versions of the soldier together because of the bitterness he felt over the Silurians.

However, that memory was also colored by the shock he felt at seeing the Brigadier get shot, his body falling to the ground, lifeless. It was one of the last things he saw before that world was consumed by a molten river of flame and the people around him were engulfed by it.

The Doctor flinched at the recollection. He hadn't been able to save any of those people. A whole planet had died screaming partially because he could not find a way to convincingly warn them of the danger they were in. Yes, he was familiar with the consequences that could happen by making the wrong decisions too. Nevertheless, until this moment, he hadn't thought that the Brigadier could relate to the weight of that responsibility.

It also occurred to him now that the shock he felt when that Brigadier was killed was partially borne out of regret. True, that Brigadier had treated him terribly, but they had been friendly enough in this world. Surely, there had been some part of that soldier who carried the same finer qualities that this one did. Had he really allowed one misguided decision on the Brigadier's part to shatter his belief in the integrity and heart at the center of his being?

The Doctor glanced over at the Brigadier, who continued to watch him unobtrusively. He suddenly realized that he had not responded to the question put to him for a long time and that it wouldn't have been difficult for the Brigadier to perceive that he was grappling with some kind of internal conflict. Still, the Brigadier showed no sign of his patience wearing thin or of any desire to press him for details he was not comfortable with divulging.

It was then, for perhaps the very first time, that the Doctor wondered if he had severely underestimated the man sitting across from him.

"Doctor," the Brigadier said, finally breaking the silence. "I am aware that you are trying to repair your TARDIS with the intention of leaving as soon as you complete your task. While it's true that I will consider it a great loss to UNIT when that happens, I can appreciate your frustration at having lost your freedom to come and go as you please."

"Can you?" the Doctor said, making sure to look him in the eye. "Can you really appreciate what it means to me, Brigadier Lethbridge-Stewart?"

"Perhaps not entirely," the Brigadier said. "But let's just say that I can understand that it is easier to make a difficult decision when you know that you had made the choice to let yourself be involved in a situation. It's far harder when you have lost the ability to walk away before reaching that point."

The Doctor blinked. Truthfully, he was surprised that the Brigadier had been able to make such an apt comparison between his position and what he assumed was the reality of life within the chain of military command. The more he thought about it, the more he was forced to admit that there was a lot of wisdom behind those words.

A trace of a smile appeared on the Brigadier's face, and the Doctor could sense that a moment of camaraderie had been achieved at last.

"As it stands, Doctor, I'm afraid that you'll have to learn to trust me," the Brigadier said. "This arrangement cannot work if I have to fight you at every possible juncture."

"You can't expect me to always agree with your perspective," the Doctor said.

"I never thought that for a minute," the Brigadier countered, the smile working its way onto his face again. "But I believe that if you put that great mind of yours to the task, you'll find a way to work around those differences. And perhaps in time, I will as well."

The Brigadier started to tilt his glass back to finish what was left of his drink when the Doctor picked up his own glass. He waved it toward the Brigadier, and the soldier responded by making an identical motion.

"To the future of our partnership then?" the Doctor said, the corners of his mouth turning upward.

"Yes, why not?" the Brigadier nodded. "I've always believed in remaining positive while moving forward."

The Doctor chuckled and took a long drink. He had to admit that the scotch was very good indeed. Once they had finished their drinks, the Brigadier stood and collected everything onto the tray before retrieving his baton.

"Good night, Doctor," the Brigadier said as he left the room. "Oh, and I'll be stopping by tomorrow with those forms you have repeatedly failed to fill out for my reports. I will expect you to make yourself available."

"And a good night to you too, Brigadier," the Doctor replied. It was meant to be a sarcastic retort, but there was too much humor in it to be truly genuine. A fact that escaped neither man's notice.

After one last smirk, the Brigadier left the room, shutting the door behind him. The Doctor swiveled on his stool and went back to looking at the sky outside his window. He was no closer to ending his exile on Earth, but maybe he had just gained something he hadn't anticipated.

And that was proof enough that he had plenty to hope for in the future.