Title: Assumptions
Author: Kylia
Fandom: Stargate: Atlantis
Genre: First Time
Relationship(s): John Sheppard/Rodney McKay
Content Rating: PG
Warnings: John Sheppard being Forward; Astrophysicists making assumptions
Word Count: 4700
Summary: John and Rodney talk


“You want me.”

“I want you to what?” Dr. Rodney McKay asked without looking up from the results he was analyzing on his laptop.

“No what…you want me.” Major John Sheppard repeated putting emphasis on ‘want’.

“Excuse me?” McKay finally looked up at the major.

Sheppard was leaning just inside the door to McKay’s lab, an insufferably smug expression on his face.

“You heard me,” John said as she stepped closer. “Twice.”

“Yes, I heard you but you couldn’t have said what I thought I heard.”

“Why not?” John asked with deceptive casualness.

“Because even you can’t be that egotistical,” Rodney said turning back to his laptop.

“Now Rodney, you know as well as I do that between us, you’re ego is larger than mine.”

Rodney sighed in exasperation. “Go away, Major.”

John stepped closer, staring at the scientist with an intensity Rodney hadn’t seen aimed at him before. “You know it’s true, and so do I. Sooner or later you’re going to have to admit it.”

Rodney snorted. “Not likely.”

John smirked as he moved back towards the door. “Think about this. We live in fairly close quarters and spend more time together finding ways to battle the Wraith than we do doing anything else. You can’t get away from me, and deep down, you don’t want to. Everywhere you go, I’ll be there, watching you, waiting…” He turned around and headed out the way he came, leaving Rodney gaping after him.


Rodney stared blankly at the diagrams he had been trying to study. After a moment, he sighed in frustration, irritated with himself for allowing John’s game to distract him.

At first, Rodney had tried to forget the major’s bizarre visit to his lab a few days before, but the more he tried to forget about it, the more he found himself thinking about it. He knew that most likely John was trying to rattle him.

Their team had been grounded for the past ten days due to a breakout of the Pegasus version of the measles. It wasn’t serious, and only affected about one percent of the population of Atlantis, but Aiden Ford was one of the one percent, so Dr. Weir had put them all on stand down until the illness had run its course instead of assigning someone else to their team.

Rodney had actually enjoyed the downtime, it gave him some time to go over a couple of experiments he’d been working on with an unusual metal alloy found on Atlantis. The alloy wasn’t Naquada or even anything similar and seemed to react with salt water as well as a number of other common liquids.

Teyla had gone to the mainland to visit with her people, which left the major at loose ends, apparently. John had probably gotten bored and decided to occupy himself with his favorite pastime, annoying Rodney.

At least, that’s what he had thought at the time. However, it had been three days since John’s visit to his lab. Three days in which Rodney could almost feel John watching him anytime he ventured out of the sanctuary of his lab.

MacKay was now beginning to believe the major had been serious, at least about his intentions to pester Rodney until he admitted that he did, in fact, want John. The scientist was getting rather annoyed.

It was bad enough that John had just assumed that Rodney would want him, that Rodney couldn’t help wanting him, but the fact of the matter was, he was right. He did want him. Smug bastard.

To confuse the matter more, Rodney couldn’t figure out what John’s angle was. He knew there had to be one. In his experience there always was. People, whether male or female, did not approach Rodney McKay on any kind of personal level without a reason. He wasn’t exactly people friendly and wasn’t naive enough to consider himself attractive.

That’s not to say Rodney was inexperienced. Quite the opposite in fact. It was just that all of Rodney’s past partners had had an ulterior motive in approaching him. From the girl in junior high that had asked him to a dance on a dare, to the pre-med student who needed help with math when he was an undergrad.

Even the liaison to the Stargate program in Russia had only wanted to pick his brain on the inner workings of the SGC. In every case, Rodney had known what they were after and had had his own motives in return. Mostly he hadn’t minded because so much of his life surrounded his work that he didn’t have time for the melodrama inherent in any kind of real relationship, with either sex.

This was different though. As of yet, Rodney couldn’t figure out what John’s motive could be. He didn’t have anything the major would find useful and though the major didn’t know the ins and outs of most of the ancient technology, he had no desire to learn. John Sheppard didn’t care how something worked, only that it did. And for John at least, getting Ancient technology to work wasn’t a problem.

Rodney wasn’t without his charms when he chose to employ them, but very few people could claim to know what exactly those charms were. He was admittedly arrogant and stubborn, and an ass more often than not.

What then could John Sheppard want with him?


Rodney left his quarters during the middle of the night, having spent more time thinking than sleeping. It had been six days since John’s impromptu visit to his lab. While the major wasn’t exactly stalking him, neither was he avoiding him.

In fact, true to his implied threat, John was always just there. When Rodney came out of his lab, John would be there, walking the hallways with the scientist on the way to his quarters or the mess, making inane conversation.

Sheppard hadn’t made any more advances if one could call it that, but he would watch Rodney with the same single-minded intensity he had exhibited that night. Almost as if he was waiting for something. Waiting for what exactly Rodney couldn’t say.

McKay was starting to feel a little isolated and more than a little claustrophobic, trying to limit his contact with the major as much as was currently feasible. During the day it wasn’t really a problem. He was too busy with his work, working on various experiments, and trying to understand just that little bit more of the Ancient technology. However, sometimes at night, it seemed as though the walls were closing in on him.

Tonight was one of those nights.

He wasn’t sure where he was going, just as long as he was away from his quarters. Rodney wasn’t really paying attention to the halls and corridors he turned down, not really caring where he ended up, until he stopped suddenly, realizing where he was.

There was a light up ahead, a few meters away. The light came from the walls in the corridor and usually only activated as you walked near them. Rodney looked more closely at the lighting. That’s when he noticed the lights were on either side of the door to John Sheppard’s quarters.

The officer in question was leaning against his closed door, one eyebrow raised in silent question. Rodney could just make out the smug expression quirking his lips.

The astrophysicist abruptly turned around and went back the way he came, paying more attention to his whereabouts and didn’t stop until he was safely ensconced in his own quarters once again.


Major John Sheppard returned to what passed for his living room still smirking. Things were proceeding quite nicely. Soon, Rodney would say something, maybe even do something. It just wasn’t in Rodney McKay to ignore things until they went away.

John had spent a great many years observing. Observing people, places, events…it enabled him to assess a situation, tell when something was going to go very wrong very quickly. This time hopefully it would tell him when something was going to go very right.

Something about Rodney McKay had struck him from the moment they met. Contrary to what most people would believe, this impression had not changed once Rodney opened his mouth. Quite the opposite.

Rodney intrigued him. The man was undeniably intelligent, maybe smarter than anyone John had ever met. He was also annoying, arrogant and without a doubt the most pig-headed individual John had ever had the misfortune to work with. He was sarcastic and rude, self-centered and snarky.

John thought that maybe he was in love.

It had never happened before, but there was always a first time. Right?

Over the years he had had his share of lovers. Men in foreign countries on dangerous missions and women who had found him nice to look at and suitably charming. Some pursued him, others he casually approached. None had grabbed his attention like this, and drawn him in, completely confounding him at every turn. Every time he thought he had McKay figured out, he’d say or do something to prove him wrong.

Watching Rodney McKay had become a favorite pastime. Sometimes, though not very frequently, he could see glimpses of the man underneath the bluster.

John Sheppard wanted into the walls. He wanted more than vague glimpses. Being the tactician he was, the major had figured out the best course of action to get where he wanted, needed to be.

Enter Rodney baiting.

If Rodney’s midnight visit down the halls of Atlantis was any indication, it was working.


Doctor Rodney McKay entered what passed for the mess on Atlantis, casting a furtive glance around and sighing in relief when he noticed that there were only three other people in the room. Elizabeth had set up a sort of rotating schedule with the handful of people who had volunteered to help with growing and preparing food for their little expedition. During Atlantis’ daylight hours, there were one or two people on duty preparing or serving food according to a menu someone had taken it upon themselves to draw up. At night, there was no one on duty, but leftovers from earlier in the day were available for anyone who hadn’t eaten. It seemed more practical than having set meal times, considering many of the scientific departments worked what would be considered odd hours back on Earth. Though Atlantis time and Earth time weren’t exactly the same, most members of the expedition continued to think of their day only having twenty-four hours and their year only three-hundred and sixty-five days.

Rodney didn’t actually pay much attention to how long a day actually was. Most of his time was spent locked inside a lab unless they were off-world on a mission, in which case they weren’t on Atlantis time anyway.

These days he would have been perfectly happy to spend all his time in his lab, however, he still had to eat and though they did have a mess, they didn’t have delivery. Mostly he was working on various experiments, and trying his best not to completely alienate the other scientists under his command, though some days it was a near thing. Lately, however, quite a bit of his time was spent actively avoiding Major Sheppard.

He knew that eventually, he’d have to talk to the man, about what was, or wasn’t, going on between them, probably sooner than later considering their first mission since Ford’s illness was scheduled for 0900, in three days. Rodney was pragmatic enough to know they couldn’t work the way things were going now. John hadn’t actually said anything more to him, but there was enough that wasn’t said. In the silences between them when they were together, in the looks John gave him when Rodney pretended to ignore him, even in between the lines of conversations they managed to have, whether they were alone, or not.

McKay knew that he’d have to say something since it was clear John wouldn’t, but he hoped to avoid it for just a little longer, which was why he was going to find something to eat in the middle of most people’s sleep cycle. The astrophysicist grabbed a plate of what passed for dinner and took a seat in one of the empty tables in the corner of the room. He opened his laptop on the table next to the tray and began scanning the data on the screen for the fifth time. The results of one of his recent experiments for an artifact they’d recently brought back didn’t make any sense.

Every once in a while, Rodney took a bite of something he thought was supposed to be macaroni and cheese but otherwise concentrated on his work. Nearly thirty minutes had passed when he felt an itch centered on the back of his neck. He didn’t even have to turn around to know what it was. It was that same feeling he got any time Sheppard was near. He sighed slightly and straightened his posture. The time for avoidance was apparently over.

“Major,” Rodney said without turning around. He heard footsteps near his table and shifted slightly, not turning around, but moving enough to see movement in his peripheral vision. He absently noticed the other occupants of the room had apparently left while he was working.

“McKay,” John said as he came around the table and sat down, opposite Rodney.

The scientist looked up and met John’s eyes for the first time. His face was blank but Rodney could see that familiar twinkle in his eyes. “Okay. You win.”

“I do?” John asked, acting as if he didn’t know what Rodney was talking about. “What do I win?”

Rodney scowled. “Nothing.” He paused before continuing. “I will admit to finding you…” He couldn’t quite finish the sentence, especially when John’s lips quirked upwards like that.

“Hot? Irresistible? Fascinating?” John offered his own adjectives.

“Annoying.” Rodney finally said. It wasn’t quite what he had meant, but it was true nonetheless.

“You too,” John said seriously, agreeing both to what Rodney had vocalized, and what he hadn’t.

“What do you want?” Rodney growled, hating this weirdness between them now.

John shrugged. “Power for Atlantis, an end to the Wraith threat, new episodes of Pinky and the Brain. What do you want?”

Rodney opened his mouth to say ‘for you to leave me alone’ before shutting it, realizing it wasn’t true and he wasn’t willing to lie outright. While he was thinking of something else to say, he rewound John’s statement. “Pinky and the Brain? And here I was thinking you were more of a Sponge Bob fan.” He shook his head and looked at the major seriously. “What do you want?” He asked again.

“Same thing you do.”

“And what might that be?”

John smirked slightly. “To get naked and horizontal in a place a lot less public than this.” He stared intently at Rodney before adding, “Together.”

“And what makes you so sure that’s what I want?” Rodney asked, not even attempting to claim he didn’t sleep with men. John had no doubt read his file.

Sheppard smiled, not a smirk, or even a leer, but a real smile. “I noticed, Doctor McKay, that you haven’t once denied that you’re interested, not even that day in your lab. You haven’t come right out and said no either. Why do you suppose that is?”

“Because I’m a nice guy?” Rodney snarked, sarcasm dripping from every syllable. John merely raised an eyebrow. “Okay, so I’m not a nice guy. I’m an asshole, which makes me wonder why you’d even want to sleep with me.” He raised a hand when it looked like John was going to speak. “It doesn’t matter. Even if I did want you, which isn’t even up for discussion, I’m not sleeping with you.”

Sheppard decided to ignore Rodney’s ambiguous admission and asked the more important question. “Why not?”

Rodney sighed, closed his laptop and stood up. “Because we have to work together, and while you are nice to look at, I’m not risking what we’re trying to do here for a one-night stand, or even a string of them.” He turned to leave before John could say anything more, hoping the major would just drop the whole thing.

Sheppard watched him go, staring at the tense line of Rodney’s shoulders as he stood up to leave himself, knowing that whether he had realized it or not, McKay had just given John an opening. Now all he had to do was take advantage of it.


“Lieutenant,” Sheppard said as he entered the briefing room.

“Sir.” Ford nodded as the major slid into the seat across from him.

“Are we early or is everyone else late?” Sheppard asked looking around the otherwise empty room.

“Everyone else is late,” Ford answered. “Dr. Weir was called down to Beckett’s office, and Teyla went with her. Something about some strange new variation of that bug that was going around the mainland.”

“Where’s McKay?” John asked looking around the room again.

Ford shrugged. “He probably lost track of time, again.”

“Yeah, he does that.” John smiled slightly thinking of the missing astrophysicist.

“Major…may I speak freely?” Ford asked hesitantly.

Sheppard looked over at his lieutenant with narrowed eyes before nodding cautiously.

“Is there…something going on between you and doctor Mckay?” Ford asked quietly.

“Would that bother you?” Sheppard asked, more out of curiosity than a real concern.

“No, sir.” Ford answered quickly.

“But?” Sheppard prompted.

“But…others might,” Ford said, looking his CO in the eye for the first time since this awkward conversation started.

“Because of Don’t Ask-Don’t Tell?” Sheppard guessed.

Ford smiled then. “No, because Doctor McKay is…” He trailed off.

“An acquired taste,” Sheppard answered for him. “I know.” He smiled slightly. “But the other thing won’t bother people?” Sheppard asked, realizing that Ford had a better handle on the military staff than he did, on a personal level. As the highest ranking military officer, he tended to get kept at a distance.

Ford shrugged. “We’re out here, for who knows how long, eventually people are going to start pairing up. Some already have. Besides, those of us that have worked with the SGC are used to a certain amount of…familiarity between certain commanding officers and their scientists.”

Before Sheppard could question exactly what that meant, Teyla and Elizabeth returned, taking their seats. “Where is Doctor McKay?” Teyla asked.

“Here, I’m here,” McKay answered as he took his own seat, looking around the table. “What did I miss?”


Lieutenant Ford took point, after orders from Sheppard, keeping an eye out for any hostile movement.

When Teyla and Ford had gotten far enough away to be out of earshot, Sheppard turned slightly to look at Rodney. “You know, you’re making a few assumptions.”

“Excuse me?” McKay asked turning to the major.

“You’re assuming you know what I want.”

“Major, according to you, what you want, is me.” Rodney pointed out. “Unless I misunderstood, and I’m pretty sure I didn’t.”

Sheppard rolled his eyes. “You’re assuming that I want a one night stand.”

“And you don’t?” Rodney asked disbelievingly.

“Rodney, I don’t do casual.”

McKay snorted. “What about that girl on PPX-369? And the chieftain’s daughter on PX3-459? That warrior on PC4-895? And the eyes you were making at Sora? Are you trying to tell me you wanted to settle down with them? All of them?”

“That’s different. I was just being…friendly.” Rodney stared at him dubiously and he sighed. “Okay, maybe I do casual, but that’s not what I want with you.”

Before Rodney could respond one way or another, Teyla called them, and John realized this discussion would have to be finished some other time.


It was several hours later when Rodney heard the knock at his quarters. He was almost surprised that Sheppard had waited not only until after the debriefing but given the scientist enough to time to shower, though not dress completely.

“What?” Rodney snapped as he opened the door. He was still damp from his shower and his hair was sticking up in odd places. He was wearing a pair of old sweatpants but hadn’t gotten around to putting a shirt on yet, and though he wasn’t in the mood to go three rounds with the major, he wasn’t nearly as irritated as he thought he came off.

“Rodney.” John nodded stepping into the room without an invitation. As far as he was concerned the fact that Rodney opened the door was enough. The astrophysicist had to have known that Sheppard would be making an appearance.

“John.” Rodney walked away, heading towards the bathroom to return the towel he still held in his hand. “What do you want?”

“You know what I think?” John asked, ignoring McKay’s question.

“That you’re God’s gift to women…and men?” McKay offered as he hung up his towel, spending more time than necessary doing it. “Have I told you I don’t believe in God, Major?”

“That you want me,” Sheppard answered as if Rodney hadn’t spoken, again. “You really want me, and you’re just realizing that I want you too, for more than just the sex, though I’m sure that will be fantastic.”

Rodney froze between the bathroom and the central living space. John wasn’t wrong, not completely, but what had him stopping was John’s use of the verb ‘will’ as opposed to ‘would’. Assuming Sheppard had an understanding of the English language, that implied that the major knew that there would be sex between them at some point.

Unlike what Sheppard tried to pretend, and what most of the other scientist bought into, Rodney McKay knew John Sheppard was a lot smarter than he claimed. Which of course was another reason why Rodney should not, under any circumstances, do what he was thinking about doing.

Smart people were a turn on, and despite his own personal experience with matters of a sexual nature, Rodney knew this more than John’s beauty would be what did him in.

Scarier than John knowing that they would be having sex at some point in the future was that Rodney knew it too.

McKay stepped closer to the major, eyeing him carefully, trying to think of all the reasons why this was a really bad idea, and subsequently discarding them all, the scientist pushed John back until his legs hit the bed.

Before John could say anything, if anything was, in fact, forthcoming, Rodney’s lips sealed over his, thereby making any questions, had there been any, moot.


Rodney opened his eyes carefully. He didn’t want to move, he was entirely too comfortable, wrapped up in a combination of blankets and warm limbs. However, moving was inevitable. Aside from the fact that it was morning, and he should be getting up, there was the fact that he had an air force major draped across his body.

Before he could try and quietly maneuver himself out from under John, Rodney felt a puff of warm air against his chest.

“Stop it.” The words were mumbled into Rodney’s chest.

“Stop what?” Rodney asked as he climbed out of the bed, not trying to be quiet now that he knew John was awake.

“Over thinking everything.”

Rodney froze a foot away from the bed, standing completely nude in his own quarters, realizing belatedly that he hadn’t been thinking about how he had woken up, though he should have been. For the first time since this whole mess had started, Rodney realized he hadn’t been thinking, at all, just feeling.

He wasn’t sure if that was a good thing or not, but he thought he liked it.

“Do you have to think everything to death?” John asked sleepily.

When Rodney turned to look at John he noticed his hair was in more disarray than usual. He wanted to smile, but instead just raised an eyebrow at John’s question. “That is part of my job.” He pointed out with irritation he wasn’t feeling.

John blinked. “Yes, and normally that’s one of the things I love about you, but right now, I don’t want you to think.”

Rodney stared at John in surprise. “What did you just say?”

John sat up against what passed for a headboard. “I don’t want you to think?” He offered in slight confusion. It was way too early in the morning to be having a conversation with Rodney McKay. Any conversation.

“Before that.” Rodney stepped closer to the bed, temporarily forgetting about his nudity in the wake of what he thought John had just said.

“Yes, thinking is part of your job.” John guessed, still not quite understanding what had Rodney looking at him with that expression on his face.

“After that!” Rodney snapped, though the expression on his face hadn’t changed.

“Um…” John reran the conversation over in his head. “I love you?” He said quietly running a hand through his hair.

“Do you?” Rodney asked just as quietly stepping closer to the bed.

“Yeah, I think so.” John sighed. He looked up at the scientist. “You’re not about to tell me why this is a really bad idea, are you?”

Rodney finally sat on the edge of the bed, sighing himself. “It is a really bad idea.”

“Why?” John asked simply, tired of trying to outmaneuver Rodney. This wasn’t an exercise.

“Because you’re…well you, the commanding military officer on Atlantis, and I’m well…me, an ass more often than not, who generally pisses everyone off, yourself included in case you’ve forgotten.”

“I haven’t,” John answered. “And you’re right, you do piss me off, frequently, but you also make me think, and laugh.”

“What about Weir, and Ford and Teyla? This is a small city, we can’t keep this a secret forever.”

“You’re making assumptions again. Who said I wanted to keep it a secret? Aiden and I were talking earlier. He said some things…we’re a long way from Earth…maybe we can leave some of the more archaic things behind.”

“I wasn’t talking about that ludicrous Don’t-Ask-Don’t-tell policy, John. Wait…you talked to Ford about us?”

John felt ridiculously pleased and something like a school girl wanting to jump around saying ‘he said us’. Instead, he just smirked slightly. “Us?”

“Okay, yeah, us,” Rodney admitted. “You spoke to Ford about us?” He asked again.

“Sort of,” John answered. “If you weren’t talking about Don’t-Ask, Don’t-Tell, what were you talking about?”

Rodney stood up and walked away from the bed. “I’m not the nicest guy. You’re going to get some attitude about this.”

“Haven’t you gotten it yet, McKay? For a smart guy, you’re very slow.” John said as he climbed out of the bed, dropping the sheets and striding over to Rodney, and turning him around so they were facing each other.

Rodney’s eyes made the journey from John’s bare feet, up his lean body, from his legs to his chest and everything in between, only then remembering that John had been naked in that bed. His bed. He swallowed thickly before trying to concentrate on what John was saying.


John smirked slightly, noticing the look in Rodney’s eyes. “I don’t care.” He said quietly but seriously, willing Rodney to believe him.

“Huh? Care about what?” Rodney blinked, trying to bring his mind back to what John was saying and away from his more…physical attributes.

“About what people think. I love you.” John said, a little more sure about it this time.

Rodney stared into his eyes for a moment, surprised by the look in John’s eyes. “You do, don’t you? Wow.”

“Yeah.” John nodded. “Come back to bed.”

“Okay.” Rodney allowed himself to be led back to bed. After they had gotten under the covers and John and pulled Rodney half on top of him, Rodney sighed contentedly. “I, uh…I…love you…too.”

John smiled. “That was really hard to say, wasn’t it?”

“You have no idea.” Rodney laughed a little. “Or maybe you do.” He smiled slightly as John ran a hand over his back. “You know we still have to talk about this propensity you have for talking about our…whatever…with other people.”

“I know.”

The End

One Comment:

  1. I LOVE IT. They were talking at cross-purposes for so long, but it’s nice that they end on the same wavelength <3

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