Atlantis Fanfic
Just as he did every morning, Lt. Colonel John Sheppard strolled into Atlantis central control approximately 10 minutes late, a smirk plastered on his face as his hands juggled two cups of coffee, a small breakfast, and a small, non-descript box. Awaiting him was none other than Dr. Elizabeth Weir, standing there looking to the world every bit the impatient boss, but John detected a hint of a smile playing at her lips as she stood waiting in the early morning crowd of the control room.
"Well, it's about time you graced us with your presence, Colonel. I was beginning to think you had gotten lost, or forgotten our little arrangement where I let you take out jumpers for casual, scenic flights and you agree to be akin to Rodney's lab rat."
He pretended to drop the coffee in mock horror, and promptly replied, "Damn, I was hoping the free breakfast would incense you to talk him out of that. The last thing I want to do on my first official day off here is play Rodney's guinea pig. At least I have breakfast to look forward to." He said as he walked towards her office, set the coffee and breakfast on her desk, then sat in the chair, leaned back, and watched her as she walked into the office.
"Why Colonel, if I didn't know better, I'd say you were afraid of our dear Rodney." She mock formally replied, then changed her demeanour instantly as the aroma of the coffee and cream cheese covered bagel infiltrated her senses. "Seriously though John, this is nice. And while it may not get Rodney off your case, I promise next time I will personally drag Beckett down to Rodney's lab and order him to cooperate. Thanks for breakfast."
He only smiled as he took a bite of his bagel and looked at her cluttered, organized desk. He supposed there was some order to the madness, but he couldn't discern what made the piles different from each other, other than their varying heights. He picked up a file, opened it, and perused the contents. The report was fairly boring, a standard application form for bringing materials to Atlantis from Earth on-board the Daedalus, and it looked like one Dr. Matthews was requisitioning some chemical he couldn't pronounce, for the explicit purpose of 'research'. He snorted and when Elizabeth looked up, she frowned slightly.
"You know, you don't exactly have the authority to look over those. You know how much trouble we would both be in if the SGC or the IOA got word that you could just walk into the expedition head's office and sort through the files at your leisure? And not to mention the expectation of privacy that everyone here would like to enjoy in their requisitions."
He looked back, directly at her, slightly exasperated. He closed the file and replaced it back on her desk, looked up at her, and began to speak.
"Ok, first of all, I am Atlantis' military leader, and it states in the international agreement-" He received a raised eyebrow and a hint of a smile after that particular statement, and he continued, "-that as ranking military head, I may, at my discretion and at the expedition head's convenience, peruse any file for the purposes of assessing the legitimacy of actions, the chance of success in the endeavour, and pointing out any strategic flaws or liabilities that may occur as a result of said actions." He finished with a flourish.
Elizabeth tried to interrupt him, but John raised a hand to forestall her request and continued his tirade.
"As well, Atlantis is much more like a family or close knit community than an actual city, at least on Earth. I stress you to find one person –minus Cavanaugh who would object to a little bending of the rules here and there for the betterment of anyone."
Elizabeth had to agree. These past few years on Atlantis had seen wraith, replicator, and Genii attacks, all of which, while horrible acts in themselves, not to mention the fallout and loss from them, really did bring the city together as one. In fact, she was sure that many members of the expedition were doing some things that weren't exactly forbidden, but frowned upon. Ah, the bliss of rumour and plausible deniability. She tuned back into Sheppard's conversation before he started again.
"And finally, these requisition forms? Due to the fact that they could conceivably contain hazardous materials, illegal substances, or restricted items, I get a copy too." He finished and gave her his patented John Sheppard I-am-so-right-and-cute smile.
She laughed in response and said, "Very well Colonel, touché. I am surprised you got through all the legalize of that agreement and deciphered it's true meaning. However, I thought you needed the head's convenience to peruse a file, and I seem to be rather busy eating a distraction oriented breakfast with one military head." She crooked her head and raised an eyebrow, wanting to know what he could come up with in response to that.
He didn't disappoint. "What, this a distraction? No, not at all. In fact, the reason for this visit is purely without ulterior motives." She glared at him and he sighed, "Well, mostly without ulterior motives."
She sighed then as well, and responded, "I know, Beckett has you looking out for me. And while I am extremely annoyed about that fact, somehow it doesn't seem so bad when it results in this." She spread her hand out over the somewhat limited but extremely heartfelt breakfast before her. She then spied the package that John also carried in with her and promptly pointed it out.
"And what, pray tell, is that, Colonel?" She asked, pointing toward the box he had half-hidden behind the few things that adorned her desk.
"Oh this little thing," He started with a smirk. "Nah, you wouldn't be interested in that. Regardless, I know you, so don't open this until you have a moment to yourself. Is that explanation enough, oh fearless leader?"
She smirked as well and, for some reason she didn't fully comprehend, she stuck her tongue out and made a lunge for the package. He seemed to be expecting this though, and moved it away with one hand while his other held down her incriminating hand. Curiously, the noise in the control room dimmed and went out altogether. They were both staring at each other in a peculiar fashion, and John could have sworn that Elizabeth had mouthed out something under her breath, but he didn't know what.
He was about to respond when their radios crackled to life and both of them quickly dropped and changed their posture as if caught doing something they weren't supposed to. They were both secretly glad that their now pink-tinged faces could not be seen except by the other, as they listened for the incoming message.
"Dr. Weir!" Said a somewhat agitated Rodney McKay.
"Yes, what is it Rodney?" She responded somewhat impishly, knowing the reason for his call was sitting across her desk, silently laughing.
"Is Col. Sheppard with you? I can't seem to find him. I checked his quarters, the gym, the mess hall, and I was going to check the control room, but Radek found some interesting subroutines in Atlantis' mainframe computer and I was redirected to the chair room."
"Yes Rodney, the good Colonel is sitting right across from me."
"Well what the hell is he doing there? We don't have all day! Tell him to get his ass in gear and come down here immediately, I can't afford to wait any longer, my time is precious you know."
"All right Rodney, but I do need you to calm down a little. I can't knowingly send John into your clutches only for him to return frazzled and unable to defend the city."
"Yes, yes, just get him down here already. What else could he be doing? It's his day off, it's not like he has anything else to do."
"I'm sure the Colonel has his own agenda for the day, Rodney. I need you to remember that and have him back here in no more than 3 hours, understood?"
"Oh common, Elizabeth! 3 hours? At this rate, it will take Sheppard that long just to get down here. You can't possibly be-"
He was cut off at her curt reply, "Yes Rodney, I am serious. You have him for 3 hours, as soon as he steps inside the chair room. No more." She finished with a tone of finality.
"All right, all right, just get him down here now, McKay out."
The transmission died with a slight click and the two leaders were left in Elizabeth's office. At first, both looked to the eyes of the other, and for a moment, they shared that same inquisitive look. As they broke away, this time with no blushing to be seen, an unspoken something passed between them, instantly understanding each other.
John got up to leave with a smirk on his face. "Wouldn't want him to blow up part of the city in retaliation, now would we?"
She smiled as he departed, and while thinking about what had just happened, she still heard the last thing he said before he left 'And I thought War and Peace was annoyingly long-winded'.
"So, what delightful little experiments will we be doing today upon Atlantis' little guinea pig?" Sheppard called out as he reached the chair room in one of Atlantis' many dizzying towers.
"Ah, Colonel, finally got your ass in gear and headed down here? I can't believe you hoodwinked Elizabeth into that whole 3 hour cap thing. What else were you going to do today?
"Oh, I don't know McKay. I was thinking of reading, golfing, maybe taking a trip to the mainland or perhaps just kicking back with the Man in Black. You know, what ordinary people do on their days off, at least the ones who have a life."
"Ha ha Colonel, very funny. Let's see if I can relate this to your mind. You. Sit. Here. Now." He emphasized each word with a jab of his finger in the direction of the chair.
Sheppard moved toward it, saying hi to Zelenka as he passed the Czech, who took almost no notice of him as he was saying something, probably swearing in his native language, while staring at a computer readout. He sat down in the chair, and instantly it fell back into a reclined position and John felt himself connected to every part of the city. He could tell, for instance, that there were two people in the gym, seven in the control room, and 22 in the infirmary. He winked the lights on and off, as he was prone to doing whenever he inhabited the chair, causing the usual moaning from everyone trying to get on with their day.
"If you're finished with your childish antics now, Colonel?" He didn't wait for a reply. "Ok, now we found some subroutines the other day that activate some buried and highly protected programs of the Atlantis mainframe. Can you detect them?"
"Yes," He replied in his dreamy, detached tone that he took whenever he was interfacing with the city.
"Ok, now listen very carefully. I want you to remove the protection one layer at a time, but do not activate anything until we have had a chance to look it over, understood?"
He simply nodded and began his task. The first program was of little importance, as he pushed aside McKay's discovery protocol like it wasn't even there. He examined the files, and saw that there was no visible way to remove the protections without triggering the incineration subroutine common to those files specifically.
'Comon, Open Sesame?' He groaned in frustration as he tried to covertly open them, and then received a message that he was sure was in ancient, but he understood.
'Identify yourself, or this section of the database will be erased. You have thirty seconds to comply with the proper pass-phrase or this information will be deleted.'
"McKay," John shouted out, audibly this time, as he could see a clock counting down in some part of his awareness. "We have 28 seconds until this part of the database incinerates itself, any idea what the pass-phrase is?"
"WHAT?" McKay shouted, as he hustled over to Zelenka's workstation and promptly told him to move. "I said not to activate anything, Sheppard. Please tell me you listened."
"Keep your socks on McKay. I was just trying to remove the protection surrounding it, one layer at a time, like you said. Any idea on the pass-phrase?" He stressed.
"Your guess is as good as mine right now, Colonel."
John just swore silently to himself and returned his full attention to the files and the clock. 'Umm, stop, please?' Not surprisingly, the countdown kept going. 'Great, well that worked. I wonder what else could be a pass-phrase?' The clock was at ten seconds now, and still counting towards incineration. 'Ah hell,' John thought 'It could work. This is Lieutenant Colonel John Sheppard of the United States Air Force, Earth. I request you stop this countdown at once.' The countdown stopped, and John could hardly believe his luck.
A voice replied, 'Welcome, John Sheppard, of the Air Force of Earth. We have been waiting some time for you to attempt to access these files. We sensed your presence here when you arrived here with the others, and opened our city to you. We were wondering when you would delve into the mainframe and attempt to bring the city back to a fully operational status. Why should we entrust our city to you?'
John distinctly felt like he was being tested, and although annoyed at this, he still felt compelled by something to answer truthfully. 'Well, a lot has happened since you guys last controlled the city. After the last great siege, at least that you know, of Atlantis by the Wraith, it lay dormant at the bottom of the ocean for roughly 10,000 years. We came from Earth, in the Milky Way, to attempt to locate this city to help out militarily at home, as well as advance our culture, understanding of you, and our level of technology so we would not have to fear attack ever again.'
'Since we have been here, the city has been attacked by the Wraith again, as well as the Asurans, thanks for the warning about them, as well as a race of humans who call themselves the Genii. All in all, it's been a weird time here, but I, as well as everyone else here wouldn't have missed it for the world.'
'On a more personal note, this city has changed from a fascinating city-ship into our home. Everyone here feels like they belong to a part of this large Atlantis family. Even some who never knew the value of family, I-well they have found a place here, a purpose in their lives.'
As John finished, he hoped it would be enough to access the files. There seemed to be some sort of conversation going on, and he felt differing… emotions? from each individual program, almost as if they were people. On second thought, after Aurora, he kept the possibility open that they could be.
'Very well, John Sheppard of Earth's Air Force. We hereby grant you full access to this city.' John smiled and was about to leave that region of the mainframe when a collective voice shouted 'Wait! This will not hurt.'
John had no notice of anything around him changing, but began to feel peculiar, almost like an out of body experience. He closed his eyes and a calm, soothing feeling came over him, and he was not afraid. He know this may sound stupid to anyone else, but he trusted the city, could feel it fully now. He sighed and let the feeling wash over him.
Meanwhile, in the chair room, Rodney had been trying to contact Sheppard about those files missing, but couldn't get through to him. He silently swore to himself, and was about to cut the power and force John out of the chair when his eyes opened. Rodney took a step back and couldn't speak, as his eyes were pure white and shining. He remained for a few moments, before he vanished entirely.
McKay stood frozen agape for a second before his logical side took over.
"Control Room, This is McKay! Please, someone, anyone, come in, NOW!"
Elizabeth's cool voice responded over the headset. "Rodney, what seems to be the problem?"
Rodney, frantic now, could not keep his worry filled voice to normal levels. "It's Colonel Sheppard. He's disappeared!"
"Did he just wander when you weren't looking? Maybe he's playing a joke on you, Rodney."
"No no, he was in the chair, opening up some newly discovered subroutines that activated a bunch of bunch of protected programs. While attempting to remove the protection around these programs, he triggered a countdown to incineration."
"Well, what happened?"
"Yes, Elizabeth, getting to it. He then said he needed a pass-phrase of some sort, but I had no idea what it would be, so I told him to guess. Oh My God! What if he guessed the wrong thing and the chair incinerated him also?"
"Rodeny, let's not get ahead of ourselves here. Did anything else happen before John vanished?"
"Yes, he was conversing with something in the mainframe, and then his eyes opened. They were pure white, Elizabeth, and shining. Then, he disappeared."
"Well Rodney, I'm sure that-"
Whatever else she was going to say was cut off as the control room came to life instantly. The Stargate began powering, but it was not an outgoing of incoming wormhole. Each of the 37 symbols around the circumference began lighting up, as every single person watched on in awe. As the last symbol lit up, the Stargate formed a pearly white, transparent event horizon that was intensely bright to look at. Somewhat shielding her eyes, Elizabeth wondered what this meant.
"Can we power the shield?" She asked the gate technician. The symbols began flickering and the gate charged up again. As this was happening, the thoughts that flashed through her mind were dark, to say the least. 'What is this? Could it be another Wraith attack? Or Replicator? I'm certain the Genii have little or nothing to do with this. Why does this situation seem a little familiar?'
"No ma'am, can't see it." He replied, after squinting in an attempt to see the status of the shield.
As the gate hummed with energy, every eye was pointed in it's directly when something extremely peculiar happened. Calmly stepping through this strange event horizon was none other than John Sheppard, looking as peaceful as if he had just taken a walk. He lifted a hand in greeting, and the gate shut down. The pure weirdness of what had just happened fell on everyone in the room, and Elizabeth temporarily forgot about the voice in her headset.
conversation with Elizabeth: woman running atlantis, proposed military, johns support of her, Rodney calling in to get Sheppard down to chair
john is rodneys guinea pig
unlocks avatar creation, eyes white, in chair
Stargate activates, white event horizon that occurred in 48 hours (teal'cy)
Stuck in infirmary for look over
Avatar of atlantis formed in johns image, city tied to him, John has comical conversation with avatar john
Start of john Elizabeth relationship as serious
Defeat wraith, manipulate replicator base code to disassemble, atlantis and Pegasus galaxy turned into hospitable and free from enemies, but for how long?