Note from the author:

Hello all! Thank you for taking the time to read this fanfiction. It's a bit of a rough start, but just wait until it catches its momentum. These first three chapters are set for you to begin to understand the two more important characters—Tony and the Commander. I promise all things will be answered in due time. For now, I simply ask you bear with me as we grind through these chapters together. I can readily assure you that the strangeness of the personality of the Commander will be explained within the next installment. Enjoy!

-B

The following morning Tony went through roughly the same routine as the day before. He and David met up at the same time. They rode down into the base together, chatting about idle topics until they reached the bottom. He felt like he wasn't the only one who was disappointed that the Commander wasn't on the couch waiting for them, as David seemed to deflate a bit when he saw she wasn't there. Neither of them commented on it as they went their separate ways, only promising to go and have lunch when the time came.

Tony went through what was becoming his normal routine after that: flicking the lights on in the med bay, setting his stuff aside and out of the way, grabbing a few books and setting them aside to read, taking his notebook that contained odd facts about the different alien species from the Commander…

"What?" Tony asked dumbly as he stared down at her. "Commander?"

She looked up at him from where she was laid out across the counter, only a light crinkling around her eyes showing that she was amused. "Yes, Noobie?"

"What are you doing?" he cursed himself for asking another stupid question, sitting in his chair. "Did you need something?"

"Nope," she stretched and sat up, tossing his pen at him. "Just fixed some stuff."

Eyebrows raised he opened the notebook, immediately noting the changes. He had been writing everything out in black, but now red ink was scrawled in the margins of the page in cursive. Occasionally the red ink would mark out something he had written completely. He took his time as he read through the notebook, reading the added facts from her precise hand. He was aware she was still sitting on the counter, watching him as he reviewed the new notes. He didn't care; he was going to take his time with it. She had added at least a hundred different things throughout the pages, and a lot of them included small anecdotes about how she had encountered the species at one point in time. He was going to enjoy his new reading material regardless of how fast she wanted him to read it.

"Hell," she finally murmured, exasperated. "I forgot how long it can take you humans to read. For fuck's sake, you're taking forever."

"Well, for starters, you've written quite a bit. You also included these funny little stories every so often, which I enjoy reading. I'm going to take my time so I don't miss any details. And "us humans" tend to enjoy not being insulted when they're reading what someone else wrote on one of their possessions," Tony said defensively, only glancing up at her. He couldn't pin down her personality. Yesterday she had been cold and distant, with only glimpses of how she was on the moon. Today she was impatient and sticking around him. She made little sense, but she may be doing it on purpose. He wouldn't put it past her.

Eventually, he came to the last page, the one he had marked "Time Lord." He was disappointed to find it was mostly blank. She had added a drawing of what he assumed was the organs inside of a Time Lord, with the double hearts being the only thing different. He supposed that was useful, but he had been hoping for more.

"Oh, don't look so depressed," she finally said, watching as he frowned over the last page being blank. "I wrote some on the next page. It just wasn't related to anything medical, so I figured it didn't belong on the page with that stuff."

He didn't spare her a glance as he turned the page. His eyes widened as he took in the page. It was absolutely covered in writing and drawings, from top to bottom and left to right. He even found a bit more when he turned to the next page.

"I answered some of your questions," she told him quietly, slipping onto the floor. "Just do me a favor and don't let anyone see that, okay?"

"Yeah, of course," he replied quickly, making eye contact with her for the first time. He was surprised to find that she looked almost vulnerable. He took it as a good sign. It was a very typical response to have after giving someone something you deemed personal. He was proud of her, in a strange way. In three days he managed to glean some information about her people. He had a feeling some people may have been trying to get that from her for years. "Unless any of this information becomes of importance to saving your life, I won't tell a soul."

She snorted at that, shaking her head. "Yeah, whatever, serious McGhee. Look, I'm going off for a bit. I have some things I need to do. Just remember that I'm serious. Don't tell anyone. Hell, if I ask, don't even tell me. Alright?"

"Yeah, alright," he shrugged, shaking his head a bit in confusion. "I'm not sure I'm following why, but I'll not tell anyone."

"Good," she nodded, walking to the far corner of the room. Tony furrowed his brows in confusion at what she was doing until he saw her open a door on a cabinet he hadn't even paid attention to before.

"What are you doing?" Tony asked as she began to walk inside of it. He could barely stand to look at it for long, instead choosing to look at the wall beside it.

"What? Oh, right," the Commander drawled as she watched him, "There's a perception filter on this. It's just the TARDIS. C'mon, give her a look. The perception filter is quite a bit stronger than what's on the lift to get into the base, but if you give it some time you'll be able to look at it without wanting to look away."

Tony exhaled a breath he hadn't realized he was holding as he looked back at her within the perception filter. It was a lot harder than she made it sound. It felt like his eyes were wobbly, and his thoughts felt like they were slowed down. Within a few moments, though, every bad thing he had been feeling seemed to subside, and it was a lot easier to see her and the TARDIS.

"Yep. Easy," she approved before entering and shutting the door behind her. A few seconds later, it began to disappear.

Tony shook his head at her strange behavior, swiveling his chair back around to continue reading the notes she had made in his journal. He was surprised when less than a minute later the Commander barged in through the main door and sat herself on one of the beds in the room.

"What, back already?" he asked her incredulously, turning around to face her.

"What do you mean?" the Commander replied earnestly, frowning at him. "This is the first I've been in here today."

Tony frowned as she said that, furrowing his brows together. Something wasn't adding up. He turned back around and grabbed the notebook, turning to the next page. He only needed to read the first paragraph to get a basic understanding of what was going on:

"Tony, you're probably reading this as you sit in confusion wondering why I insist I haven't visited you yet. I insist this because I haven't actually visited you in the correct order. The "me" you saw previously is actually from a couple of days in the future. The "me" you see now is the one most current to your timeline. Understand? I hope so, because it's going to be a bit tricky for you. I can't tell you what to do, specifically, but I can advise you. Time doesn't always move in a strict line, more often than not it's a bit more wobbly, like circles. Actually, no, time is nothing like circles. I'm not sure how else to describe it, but you absolutely cannot do anything to compromise time lines. It would be paradoxical. That would be bad. You need to keep the events that happened prior to your reading this to yourself. Don't let me know. I'll probably figure it out in my own time, or I'll probably try to beat it out of you. You'll figure out something. Good luck, you'll need it. –Commander"

Tony couldn't help but to let out an aggravated sigh as he read what she had written him. She hadn't really helped him out at all. "Well, uh, Commander, I guess I was, uh, mistaken. You weren't here this morning."

The interest that was alight in the Commander's eyes was hard to miss as she observed Tony's new behavior and the book in his hands. "Oh? I wasn't? What's in your notebook?"

"Nothing! Nothing," he replied immediately, closing it and pressing it to his chest. "Nothing at all. Don't worry about it. Did you need something?"

"Yes. I need to know what's in your notebook," the Commander grinned, holding her hands out for him to give it to her.

"Uh, no can do, sorry. It's a bit personal, it'd probably bore you to death," Tony winced as he continuously spat out lies, hoping one of them would work on her. It didn't appear like she was going to accept any of them, though. She just continued to stare at him expectantly, hands outstretched. Luckily enough for him, he didn't have to continue trying to keep it from her for very long. The rift alarm began screaming through the building, making both himself and the Commander raise their eyes to where a light flashed red in the corner of the room.

"You and I can finish this later," she said to him, hopping off of the bed she was on. "Come on, it doesn't get this loud for nothing."

The relief for Tony was palpable as he followed her out of the medical room. He wasn't sure how much longer he could've kept the notebook from her. He kept it in his hands, clinging to it like his life depended on it, and he knew the Commander had observed that. She wasn't demanding it anymore, but he knew that was unlikely to last. As soon as they had figured out what was going on, resolved it, and came back to the base she'd want it, or possibly even before that. He wasn't even sure what was going on. Why did future-Commander decide he needed this, and why couldn't he tell present-Commander about it? Oh, he was going to end up with a headache before the day was over.

They arrived in the main room as the large screen on the wall began to light up, showing a map of the United States and several red flares. Tony watched it curiously as they blipped in and out of existence, wondering what was going on. (He also briefly wondered if he'd ever understand anything going on around him.)

"Commander, we've got activity all over the northern part of the states," Abigail informed her, zooming the map on the screen in to the north. "It doesn't make sense though—none of this is centralizing. There's no way all of these places are hotspots at the same time, is there?"

"I hope not," the Commander shrugged, brushing Abigail out of the way, as she began fiddling with the computer. It didn't take very long for the Commander to violently toss the wireless keyboard several feet away. "It doesn't make sense. Did you check to make sure if there's anything in our system?"

"I would have, but it seems my keyboard is out of commission," Abigail responded, sarcasm lacing her words.

"Well, it's a good thing I checked before I broke it," the Commander said with a sigh, leaning against the desk. "Alright, well, there are three larger hotspots. We'll break apart and go to check them out. David and Abigail get New York City; Grant and Emma get Detroit; Tony's with me in Chicago. Got it? Good. We're taking the TARDIS."

The Commander left little room to argue as she swiftly moved to the opposite side of the room, swinging open both doors of her TARDIS. The rest of Lincoln was left to gather any supplies they may need during their excursion before leaving, as the Commander had already disappeared within the depths of the TARDIS' console room. Tony just shook his head at the Commander's actions, retreating to the med bay to retrieve a bag and stuff it full of assorted medical supplies. He wasn't going to be caught without something to help treat any potential injuries. He reemerged to the main room of Lincoln to see the others piling into the TARDIS, each of them with a backpack or messenger bag attached to them as if they were used to having to quickly pack and run off. He simply trailed in behind them, wincing slightly as the door closed itself directly behind him. The others were idling nearby, staying out of the way of the Commander's rushing about in the middle of the room as she began piloting the TARDIS. Tony took this time to sit down and lean against one of the railings, pulling out his notebook to read a bit more of what the future-Commander had written him.

"Now that you're in the TARDIS, I'm sure you'll take the opportunity to read some more of this," the writing began, prompting Tony to inaudibly sigh at the audacity (and, he'd begrudgingly admit, correctness) of the Commander as he glanced up at her. She wasn't even looking his way. "A lot of the things I've written in are filler—they're just there for your own entertainment. What I need you to pay attention to, not to forget, is this: I am a Time Lord. I am not a human. Do not forget that. I can handle extremes easier than you can; I can undergo more outside stimuli than humans. I do have a breaking point, as all creatures do, but that's only the point at which my body collapses. The mind of a Time Lord is infinitely larger than that of a human—" Tony pursed his lips at that, frowning at the hint that humans were inferior, "—but it can be largely occupied. There may come a time when my entire being is put into a singular cause, and when that happens I won't be able to be of assistance. Under absolutely no circumstance should you choose to stay with me if your or someone else's life is endangered by my inability to move. Time Lords can die, but not in the traditional sense. We can regenerate, Tony. Regeneration is—"

"Tony!" the Commander called, leaning around the console to see him around the glowing canister in the center, "We've landed. I'm just parking her now. You ready?"

"Uh, yeah," Tony affirmed, glancing down at the notebook in his hands in a resigned manner. He'd have to pick up where he left off a bit later, he supposed, as he stuffed it into his bag and stood up. He hadn't expected dropping off the others to take such a short amount of time. "Any idea what we're looking for?"

The Commander observed the screen hanging above her head for a few seconds before shrugging. "Not really, but that's the exciting bit, isn't it?"

"Well, I suppose. I just wish we had a bit of an idea before we go out and look," Tony told her, moving over to the doors. "I mean, it's not like we're just going to open the doors and come face-to-face with…" he stalled, noticing the peculiar look on her face as he looked back at her, "No way, really?"

"Well, you should maybe let me go out first just in case," she offered him an innocent smile as she slipped past him, gently creaking the door open to peak outside. "I sort of wasn't in the mood to wander around Chicago all day looking for something amiss; it's a pretty big area."

"So because of your own impatience you decided to land us in the middle of whatever it is we're looking for?" Tony asked her incredulously, shaking his head at the notion of it. "Isn't that a bit reckless?"

"Well, yes and no," she answered him honestly, pushing the door the rest of the way open to reveal a large tunnel. "Yes, it would be dangerous if they were online, but they aren't. We're fine."

Tony cautiously went out of the TARDIS, shutting the door behind him as he watched the Commander approach the robot-looking machine. "What is that?" he asked her, frowning as she knocked on its head to find out if it was hollow.

"Not supposed to be here, to begin with," she told him, her lips a thin line as she walked around in thought. "They're called Cybermen, though. This is an entire invading force. How did they get here? I mean, they're offline, that's obvious, but for how long? They can't stay dormant forever."

"Should we warn the others?" Tony asked immediately, pulling his phone out of his pocket. "Are these things a threat?"

"Oh, most definitely," the Commander sighed, walking back to Tony. "Cybermen are a threat. They make more Cybermen through a process called "cyber –conversion," which means they take humans and strip away everything that makes them human, leaving just a brain and nervous system to control the body," she jabbed a thumb at the Cybermen surrounding them, "This lot's already been converted. They're just dormant, which is abnormal."

"Right, well, I'll call David and have him call Grant after," Tony licked his lips slightly, his mouth having gone dry as he processed what the Commander said. These "Cybermen" were, by her explanation, humans in robot shells. Tony shook his head to clear out such horrible thoughts as he pulled up David's number and called it. He put the phone up to his ear as it rang, impatiently awaiting an answer, as he watched the Commander skitter about. She clearly didn't like these Cybermen, which worried him more than he would like to admit. He was about to give up trying to call out when a sudden and piercing beeping began throughout the tunnel they were in.

"Tony, hang up that phone! Now!" the Commander shouted, rushing over to him and tugging him towards the TARDIS.

Tony fumbled the phone as he hit end call just as he heard David calling out in question on the other line. "What is it? Commander!"

"Dormant! Won't be believing that one next time!" she yelled, throwing Tony towards the doors of the TARDIS. "Inside! Now!"

Tony pushed the doors open as he heard creaking begin all around them as the Cybermen activated, each of them beginning to advance on the pair attempting to get away.

"You will cease!" one of the Cybermen called, stepping forward from the others. "Or your companions will be de-le-ted!"

The Commander and Tony watched in shock as Grant and Emma were dragged into sight in the distance, behind the Cybermen. Tony glanced sidelong at the Commander, trying to judge what they were supposed to do, but only saw an impassive face with overactive eyes. She was looking at everything, he soon realized, observing it all at once in impossible speeds. He stood his ground as he awaited the Commander's decision, shutting the door of the TARDIS behind him.

The Cyberman leader moved forward, stiffly pointing one arm at the Commander. "You will comply! You will assist the Cybermen!"

The Commander noticeably exhaled as she took a step forward, putting on a more lofty appearance as she turned in circles to view all of the Cybermen. "And why, pray tell, would I do that? What use am I to you?"

"You are a Time Lord!" the Cyberman announced, enunciating each word in a metallic ringing voice, "You will be upgraded! You will be the beginning of a new era! Cybermen will rule all!"

"How, exactly, do you intend to start this new era? There's no one else; I'm the last Time Lord you'll run across," She raised an eyebrow in response, turning back to face the Cyberman. "You'll have one Time Lord-Cyberman and a million human ones… Oh. That's exactly what you want, isn't it?"

"Correct!" the Cyberman shouted, moving forward with several others. "You will assist! Your advanced knowledge will aid the Cybermen! You will be upgraded!"

She took a step back, towards Tony, warily eyeing each approaching Cyberman. "Tony, get in the TARDIS. Now. Don't argue with me."

Tony frowned, about to refuse and stay by her side, when he recalled what he had read in the notebook before. She would be able to resist this change, whatever it was, at least for a small amount of time. He bit his lip in aggravation as he looked between her and the Cybermen, shaking his head angrily. "Whatever you say, Commander," he agreed, thrusting open the doors and disappearing into the TARDIS, the doors shutting behind him. He could hear the metal footsteps outside as they got nearer. With a shaky sigh Tony leaned back against the closed doors, hating that he was completely helpless in this situation. He jumped forwards and off the door as he heard something hit against it. It sounded almost like, dare he imagine it, a body hitting the door. He grimaced as he set his resolve, opening the notebook once more. He quickly skimmed through the bits on regeneration, noting its importance but ultimately not finding it helpful for the more pressing matter, and found a more relevant passage.

"A strong electromagnetic shock may disrupt Cyber-systems," it read, and that was just the beginning. "Several things can produce this. The most convenient would be found in the TARDIS. The TARDIS is sentient, Tony. A living time and spaceship. She is mildly telepathic. There are never words, but emotions or ideas can be conveyed. TARDISes are grown, not made. That may seem strange to you, but you'll have to trust that it's true."

Tony leafed down the corner of the page he was on, looking around the interior of the TARDIS. According to what the Commander had written he could, in theory, simply ask for a device to take care of the Cybermen. With little resignation about how silly he may sound, he spoke up, "Uh, well, I sort of need a… uhm, something electromagnetic. I need something to take out the Cybermen."

He was surprised to hear a sort of groan from the TARDIS in response, jumping a little as a drawer slid open from the console. He approached it silently and removed the small glowing device from within it, turning it over in his hand. He assumed the button on top of it would, when pressed, release the charge. "Thank you," he told the TARDIS quietly, going back to the door and listening to the outside. He brushed aside how absurd it felt asking a ship for help as he heard the sounds of metal boots moving around outside of the doors. He frowned as he realized they were all around the TARDIS. He could faintly here voices outside, but the words were lost. The sounds of several explosions hitting the outside of the TARDIS caused Tony to jump back in alarm, briefly wondering if they could get in by force. He wasn't really too sure about how the TARDIS worked to begin with, but since he was going to be stuck in here for a few more moments he decided to see if the Commander had written any notes about it.

"TARDIS—time and relative dimensions in space. Completely organic, not just a machine. Shields capable of keeping out all but the strongest of weapons (most used by Daleks.) The shields also block most outside signals, if programmed correctly. Occasionally decides to act of its own accord…"

Tony looked up from his reading as the sounds of the Cybermen trying to get in ceased. He pocketed the notebook and moved back to the door, briefly considering just storming out and using the little device he gripped tightly in his left hand. He held it up in front of him, turning it over in his hand. He wasn't exactly sure how to use it. There are a button on what he assumed to be the top of it, but it was mostly just a plain metal canister. There were two numbers scratched into the side of it—15/20—but he had no idea what they meant. How many of the Cybermen could this thing take out at once was definitely a more important question to be asked. The next important question would be why he was the hidden away in the TARDIS to take on an army by himself. It was just his first week on the job, and he was already in way over his head.