Finding Atlantis – Chapter 4 – Keira Marcos

Content Rating:
  • PG-13
  • Discussion-Murder
  • Homophobia
  • Pre-Relationship
  • Science Fiction
Background canon relationship (McKay/Brown), Pre-McShep maybe.

Word Count:

Author's Note:
I'm doing a terrible job of estimating my word count. I have a plot. My final word count is somewhere between 30k and 300k. Shrugs.

John starts to position himself mentally to defend his son's future.

Chapter 4

He’d enjoyed flying to the mainland too much, and a meeting about the Genii was his punishment. He really didn’t think he’d ever be able to trust them, no matter who was in charge because they were mercenary and unpredictable. Ladon Radim might be less of a problem than Cowen, but a change in leadership did nothing to change the mentality of their society.

“I think they’re more trouble than their worth,” Lorne input and John relaxed in his chair. He liked his XO, especially when he was expressing opinions that they shared.

Weir’s face grew pinched. “I’d hoped that in helping Ladon secure leadership that the situation would be more positive going forward.”

“I’d settle for no hostility,” John said. “But there are elements in the Genii that we can never trust—moreover they’ve demonstrated that in the right circumstances that they could be just as much of a threat to us as the wraith. The city, as an asset, is unmatched in this galaxy and they’d take it from us if they could. We were fortunate that there wasn’t a single gene carrier among them during the foothold situation—because it could’ve made all the difference.”

Elizabeth grimaced.

“You’ve made a career out of turning enemies into friends,” John continued. “But you can’t replicate that success with alien societies whom we share nothing in common with. Mutually assured destruction goes a long way toward peace on Earth. We’ve already shown the Genii that they can invade us, kill our people, and not be punished for it.”

She flushed. “We weren’t in a position to retaliate at the time, John. You agreed it would be a mistake to attack them after they tried to take over the city.”

“I didn’t want another eager enemy,” John said. “I still don’t. I also don’t think we can trust them any further than we could throw a single one of them. Every society in Pegasus exists in a headspace between the desperate need for survival and an insatiable rage at being considered food for the wraith. Some of them respond by digging bunkers and building A-bombs. Others try to bargain, they sacrifice their old and hide their children in caves. The wraith has shaped this galaxy in ways we can’t predict and wouldn’t be able to if we lived here hundreds of years. Pegasus knows nothing but strife, Elizabeth.”

“And yet your mandate concerns you?”

“I wouldn’t consider myself a very good person if genocide didn’t concern me,” John said and exhaled sharply. “Back to Beckett’s experiment then?”

“He’s very insistent,” Elizabeth admitted. “And presented me with several parts of the expedition charter this morning that grants me the authority not only to conduct the experiment but to order you to participate.”

“You know that part of the expedition charter was voided the moment we regained our connection with Earth,” John said. “And I’d resign entirely and return to Earth before I’d willingly bring a wraith onto this city unless he’d be content with a corpse. I’ll bring him a corpse.”

“I doubt it,” Elizabeth said.

“I get that you find the idea appealing,” John said. “But it’s a no-go, Elizabeth. I’ve already communicated with both Landry and O’Neill on this subject. If the IOA approves it, then they’re going to have to arrange for it themselves without using the SGC’s resources. Not a single man or woman in uniform is going to participate in this experiment. And if anyone brings a wraith onto this city—it’ll die in the gate room.”

“The experiment truly serves no purpose as it currently stands,” Lorne input. “Even if it did work on a single wraith—we don’t have the resources or the ability to dose over a million wraith daily to keep them in whatever form Beckett has deemed suitable.”

“Unless his next step is a biological contagion,” John said grimly. “And we have to think it is. A wraith specific plague set loose on Pegasus could mutate horrifically and would probably be dangerous to people like Teyla who’s ancestors were experimented on.”

Elizabeth stood from the table. “I think you’re right—it probably is his next step, and that’s horrifying. At this point, it’s going to end up in front of the IOA one way or another. Are you sure O’Neill and Landry can prevent SGC resources from being used?”

“Yes, I’m sure,” John said. “O’Neill is vehemently opposed to medical experimentation, and any biological weapon talk will probably get Beckett recalled to Earth permanently which is probably for the best. He’s obviously not handling the stress of our situation as well as he should considering his go-to solution to our problems is this.”

– – – –

John entered his quarters pulling out his radio. He was done with the day and had already made that clear to Lorne who’d promised nothing short of a wraith siege would disturb John until morning.

McKay was on the sofa staring at his laptop.

“Already down for the count?”

“Yeah, he almost fell asleep in his elk burger,” Rodney said wryly. “I brought you some pasta back since you don’t like the elk. It’s in the fridge.”

“Thanks,” John wretched and took off his watch. “What’s up with your face? You look exhausted but also half-crazy with anxiety like we’re about to bunker down on a wraith occupied world.”

McKay laughed weakly. “Get your food, John.” He stood and motioned him toward the kitchen.

So, John went into the kitchen and pulled the box from the fridge and transferred the pasta to a bowl to be heated in the microwave. “Did he discover the meaning of life or something?”

“Better,” Rodney said. “And worse at the same time.”

John sighed. “God, Rodney, I…what did he do?”

“Oh, he just schooled Radek and me on the fact that a ZPM can’t be recharged in the method we’ve been thinking for years because what really need is a device that can capture zero point energy and place it in the vacuum space.”

John bit down on his lip. “What…how?”

“I told him he had to work on explaining how his little battery will harness ZPE and his brain about exploded,” Rodney said dryly. “And that was the result. Only Radek and I were in on the conversation, and I wanted to talk with you about it before we approach Weir with the information. It’s going to put an unreasonable spotlight on him and his research project. Kavanagh has made a very public bid to have the battery taken away from Sebastian for the good of the mission. I’m sure there are people on Earth who would agree.”


“I’ve had his research sequestered to my private server until you can get his legal rights as part of the expedition settled with O’Neill. The IOA doesn’t involve themselves in operations on that level but if we can keep a lid on the bigger picture then by the time it becomes known that your kid solved the ZPM problem he’ll have legal protection.”

“Do you think O’Neill would be okay with Sebastian’s work being taken from him.”

“No, but he answers to other people and not all of them can be trusted. Everything we can do now to insulate the kid we should because this road has no ending really.”

The microwaved dinged, so John pulled his food out and sat down at the table. “It makes me want to just disappear through the gate with him.”

“I get it,” Rodney said. “And we’ll certainly keep that as a viable option.”

“We?” John asked and raised an eyebrow. He watched McKay’s cheeks flush a little.

“We’re a team,” the scientist said defensively. “Like Teyla and Ronon would you let stroll around Pegasus without us.”

“What about Brown?”

“She’s not team, and besides I don’t think Sebastian likes her. I don’t think she’d do well on an extended camping trip in Pegasus regardless of her skills as a botanist.”

“He hasn’t mentioned a problem with her,” John said.

“She told me that he avoids her like the plague and asked me if she’d offended him somehow. I figured he’d avoid answering the question if I asked, so I’m leaving that to you.”

“I’ll just add it to my growing list,” John muttered under his breath.

“Oh, but I did get a heads up about his little side project,” Rodney said in amusement. “Not intentional on his part but I overheard him asking several different women over the course of the day if they were seeing someone.”

“Oh no.” John groaned. “Come on.”

“Yeah—he’s definitely going to try to set you up with someone. Your perpetual bachelorhood has come back to haunt you.”

“Whatever,” John said crossly and slouched in his chair. “Great, I’m going to have to come out to my kid. How weird is that?”

“Pretty weird. I mean have you ever actually come out to anyone?”

“No, most people just assume I’m gay after a while especially those who don’t know I have an ex-wife.” John grimaced. “I mean even you figured it out eventually.”

Rodney huffed. “I’d have caught on earlier if you didn’t make any appearance of being a complete womanizer.”

“Yes, well, I don’t have a choice on that front with DADT in effect. O’Neill told me in confidence that Hayes is going to repeal it by the end of the year.”

“Good, it’s a bullshit policy anyways.” Rodney cleared his throat. “Do you think he’ll have a problem with it?”

“His mother was a bleeding heart liberal who literally chained herself to trees in protest urban sprawl,” John said. “He hasn’t expressed any opinions that make me think she taught him anything drastically different from her world view when I know her.”

“Today, he told the entire science department that the pursuit of the Nobel Prize is vain and useless,” Rodney admitted and grinned when John looked at him in shock. “And said that smart people should spend their time helping others and saving the world from global warming instead of patting each other on the back for being smart.”

“Wow.” John laughed. “Yeah, that’s his mother. She inherited her grandfather’s estate about a year before I met her. She sold all of it and gave all the money to Habitat for Humanity. People she barely knew would try to lecture her for it—for throwing away her grandfather’s legacy.”

“Why do you think she kept Sebastian from you?”

“Had I guess, I would say it’s because she knew I came from money and privilege. She wouldn’t want her child to be raised with a silver spoon in his mouth. Moreover, I was honest with her when I explained that I couldn’t continue the relationship. I really tried, but there came a point where I felt that I owed us both honesty. I’ve never, ever been sexually attracted to a woman in my life.”

Rodney hummed under his breath and waved a hand. “How’d you handle that on the physical front?”

“I’d think about men to get hard and to get off,” John admitted and flushed when McKay gaped at him. “I know it’s horrible.”

“For you,” Rodney interjected hotly. “Jesus, John, why the hell did you ever try to live like that?”

“I was just trying to be what everyone wanted,” John murmured. “It just took me a while to figure out what I wanted was important. You’re bisexual, Rodney, but I’ve never seen you look twice a man on the city. I know you realize how difficult it can be.”

Rodney frowned. “Yes, well, when it comes to other men I’ve always been careful because of my military contracts. It’s easier at the SGC, of course, but you never know when you’re going to come across some caveman who wants to kick your ass for existing. I had to have more than one Marine at Area 51 reassigned for rabid homophobia.”

“One of those guys tried to volunteer to come out here last year,” John said. “But there was a note in his file from you calling him a homophobic douche. Lorne laughed his ass off. We let Landry know that we couldn’t allow anyone who’d mistreated a civilian at Area 51 to come to the city. It’s just not a good idea.”

“They like to pass their problems around to other people so they can avoid dealing with them. Landry is famous for it actually—it keeps his statistics clean which keeps his command in good standing with the DOD because they rarely, if ever, really note where problems come from when the shit hits the fan.”

“I think Beckett’s end game is a viral contagion.”

“A biological weapon,” Rodney said. “Agreed, it’s the only way to spread his ‘cure’ and make it any sort of permanent. So what happens when half a hive is infected? The remaining wraith promptly feed on the cured then they get cured abd starve to death on a hive ship with no human food. Problem solved.”

John snorted. “For fuck’s sake, Rodney.”

“Worse, the cured will probably be essentially defenseless. Did you read that part of Beckett’s proposal? He theorizes that the cured wraith will lose the memories of their life before the so-called vaccine is administered due to the physiological changes. Their brains are going to be so different that they won’t be able to process the memories of being a wraith.”

“Every time I learn something new about this experiment, the more horrified I am,” John confided. “The worse part is that plenty of people on this city and on Earth will be all for it because it looks like a solution on the surface. They don’t see the ramifications of such an experiment. They won’t even consider all the ways the thing could get out of our control and what the consequences of that would be. The wraith view us as the enemy because we interfere with their ability to feed. How they would feel about us if we started attacking their very existence? Altering their kind against their will? I’d rather not have a bunch of wraith carry a personal grudge against us.”

“It’s a fine line, isn’t it? I mean the one we’re walking. Carson’s version of genocide is so much worse than ours?”

John flushed. “I have to draw that fine line somewhere, Rodney.”

“I’m not accusing you of anything,” Rodney said. “Given an opportunity, I’d wipe the wraith out and not lose a single night of sleep. Carson, in his own way, is trying to save them from themselves.”

“Not a single one would thank him for it,” he murmured. “There are no easy answers here, Rodney, but I have to think that in their place I’d rather die quickly than be medically experimented on by an alien.”

“Oh.” Rodney sighed. “We’re the aliens to them.”


“So weird.” He grimaced then and touched his radio. “This is McKay.” John watched several emotions drift over his friend’s face, and none of them were particularly pleasant—irritation, frustration, and finally resignation. “Yes, fine, I’ll be there shortly.” He ended the call. “Katie wants to watch a movie. It’ll be some terrible chick flick, and I won’t even be able to make fun of it like when Ronon makes us watch them. Remember when he found out there was a sequel to Legally Blonde?”

John frowned. “I hate that little dog.”

He watched Rodney stand and close his laptop. “Thanks for handling dinner and everything so I could meet with Weir and Lorne.”

Rodney just waved as he left.

John finished his food, put the bowl in the dishwasher and went to take a shower. He’d had a long ass day while his son was advancing mankind with his big brain. When he’d first arrived on Atlantis, he’d let the city boss him around a little too much, and it had made him push back hard. He was starting to regret that. She obviously had needs that weren’t being met, and she was using Sebastian to get things taken care of. He didn’t know if she was influencing him mentally or not. John didn’t doubt Sebastian’s intelligence at all, but he was intimately aware of how Ancient technology could make your mind race.

He learned faster on Atlantis, but that wasn’t something he shared with anyone, not even McKay. He didn’t know how other gene carriers were impacted by the city, but he found concentrating easier, learning new skills almost effortlessly, and sometimes his intuition…well. It was hard to ignore what happened when the Genii invaded the city during the superstorm. He’d killed a lot of them—hunted, evaded, and killed. He’d been taught those skills on Earth, but on Atlantis, it all bloomed in his mind that night, and he understood what he’d been trained for on a new level. John had been able to anticipate the Genii soldiers at almost every single turn—they’d stood no chance against him no matter their numbers.

After his shower, he pulled on a pair of boxers, walked down the hall a bit to check on Sebastian then dropped into his own bed. He was exhausted but also kind of bored since McKay had left to spend time with his girlfriend. He didn’t resent Katie Brown at all. In fact, John was actually a little stunned that the relationship had lasted as long as it had and he was starting to worry about Brown’s mental health. Rodney was his best friend, but John knew from assholes and McKay was a Grade A asshole. He made a mental note to ask Sebastian why he didn’t like Katie since he was mostly curious.

His radio vibrated on the nightstand, and John picked it up with a sigh. It was the private channel he shared with McKay. “Hey.”

“I…hmmm.” Rodney sighed. “Katie got pissy with me because I didn’t want to watch some stupid movie called 27 Dresses.  She said I was selfish because she’d watched Star Trek for me and kicked me out of her room.”

“It is pretty selfish,” John admitted in amusement. “But watching Star Trek isn’t a hardship.”

“I was irritated before we even started picking out a movie because she told me that I spend too much time with you and Sebastian. She said I acted more like a parent than a mentor and I shouldn’t be tasked with babysitting your kid.” He paused. “By the way, Kavanagh called him a secret-baby which I’m pretty sure is his cowardly way of saying bastard.”

“Gah, why did we let that asshole come back?”

“I tried to veto his assignment, but Landry overruled me,” Rodney admitted darkly. “Like I said, the DOD uses him to do an end-round regarding foreign contractors intellectual property. He’s been playing this game for years which is why he fully expected to be made the CSO of the expedition. I heard he threw an epic fit when Weir picked me.”

John cleared his throat. “I appreciate your help with Sebastian, and he loves spending the whole day with you but if it’s causing issues…or gossip we can figure something else out.”

“He’s not a problem for me, and I don’t care about gossip. She’s just being ugly about it because he avoids her in a pronounced manner. I mean, even Simpson noticed and she barely remembers to get fully dressed before leaving her quarters. Sometimes one of us has to send her back to get her shoes or change them because she’s so deep in theory that putting on matching shoes isn’t even a concern. When she was working on the firmware for the gate bridge, she came to the lab twice without pants. Thank the Asgard for granny panties.”

John snorted. “The Asgard?”

“I know they exist,” Rodney said peevishly. “Also, Katie invited me to church again. I’ve told her repeatedly that I’m not religious and she just keeps trying to get…bah. What are you doing?”

“I was going to try to sleep until some inconsiderate asshole called me.”

“As my best friend, you’re required to console me when my girlfriend kicks me out of her quarters.”

“You didn’t even get laid first,” John said with a laugh.

McKay sputtered and hung up.

John plucked the radio from his ear and dropped it on the bedside table again.


“Hey buddy, did I wake you up?” John sat up and started to push back the covers, but Sebastian came fully into the room and crawled up on the end of the bed.

“No, I had to use the bathroom. Sleep’s most profound enemy is a full bladder.” He grinned when John laughed. “Did Dr. McKay tell you about today?”


“What do you think?” Sebastian bit down on his lip. “I mean…I was wondering if we could just not tell anyone that’s my idea or whatever.”

John frowned. “You know, being altruistic is one thing but allowing yourself to be taken advantage of is another. I don’t want you to ever be afraid to lay claim to your own theories or work.”

“I’m not supposed to get too much attention from the IOA.”

“It’s my preference, yes, but I’d never want you to deny yourself what you are due because of that. I have quite a bit of leverage in my own way, and I’m not above using it.” John shifted his pillows around and rested against the headboard. “McKay says you don’t like Dr. Brown.”

Sebastian frowned. “Well, she’s nice enough, and I’m pretty sure that Dr. McKay is going to ruin her life just by being himself because he’s a man-eating dinosaur and Dr. Brown is like some delicate hothouse flower. I don’t get their deal at all, but I don’t dislike her because of it.”

“Then why do you avoid her?”

“Oh. Well.” Sebastian sprawled out on the bed and stared at the ceiling. “She keeps trying to mother me, and it makes me feel gross. I don’t want a replacement mom, and most of the ladies on the city get it. She doesn’t get it, and I don’t want to be rude, so I just avoid her. I guess I’ve been rude anyways. Should I apologize?”

“No, you were right to avoid her. If someone makes you uncomfortable, you’re not obligated to socialize with them. I’ll take care of it.”

“Okay.” He sighed. “I have a thing.”

“A thing?”

“Yeah. I mean.” Sebastian sat up and turned to face him. “My mom was cremated. I had her ashes put in the creeptastic family mausoleum her great-grandparents bought. It was the last spot left, thank goodness because I didn’t want to feel guilty about not getting my remains stuck there eventually. Anyways, I kept some of the ashes. They’re in a little urn that Mr. Blake got for me. I’ve been thinking about what I’d like to do with them, and I thought we could do something together for her, here.”

“Like what?”

“I don’t know, yet. I think Mom would like it here—even with all the dangerous parts. Atlantis is amazing, you know?”

“I do know,” John murmured and cleared his throat. “You mentioned the public park a few weeks back. The one that botany hasn’t fixed. We could bring a few trees from the mainland—I’m sure the Ancients have records of what sort of trees or plants they put there originally. We could plant a tree for your mom.”

“Mom loved trees,” Sebastian said. “We’d just planted one in the backyard when…the accident happened. Mr. Blake is keeping the house for me. He’s acting as my estate manager, but you know that. He loved her, I think, but she was determined to be single forever. She said that marriage was for people who were done with actual living.”

John laughed. “That doesn’t surprise me at all.”

“I’ll ask Dr. Weir about the park in our next lesson. It would be a good community project.” Sebastian slid off the bed and stretched. “Are you sure I shouldn’t just let McKay front the big part of the ZPE stuff?”

“He wouldn’t agree, and you know that already,” John said. “And no, I don’t want you to hide. I’ll make sure you never have to one way or another. We’re going to keep it private for now while I work with some people on earth regarding a contract for your work.”

“Okay, goodnight Daddy.”

“Good night,” John said and took a deep breath as his son left this room. He wished life had an instant replay because he’d really like to go over that whole conversation again so he could figure out if he’d fucked up anything or not.


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About Keira Marcos

In my spare time, I write fan fiction and lead a cult of cock worshippers on Facebook. It's not the usual kind of hobby for a "domestic engineer" in her 40's but we live in a modern world and I like fucking with people's expectations.


  1. I do love a smart and wary John Sheppard. I love that he has his priorities set for now with Sebastian at the top. I love that he does struggle with moral dilemmas. Lots of great stuff. Thank you for this.

  2. I adored this. Fatherhood is a good look on John

  3. Another great chapter. I just want to hug Sebastian, and John. And Rodney too.

  4. Wonderful chapter. John is a good father.
    Thank you.

  5. Oooh. lol. I made an incorrect assumption. I thought you were going up on meeting the word goal, not making it explode. I love watching this place, and wandering around Facebook on the outskirts of writing communities, but I have a real phobia about word goals and would only upset myself if I tried and failed in participating. Some would call me a wuss, but I have mental problems and no desire to exaserbate them more.

    So, while a word limit is fine, if it cramps your fun, let it go this time.

  6. What is it about autocorrect that mangles a sentence?

    I meant to say I thought you were having trouble with getting a good amount of words. I should have known that wasn’t the case.

  7. McKay is a man-eating dinosaur and Brown is a hot house flower. That’s perfect. I love how you write John as a Daddy. He is beautifully realized. Rodney is so badass as a mentor. You have me on the edge of my seat.
    Thank you for being you.

  8. John is trying so hard and he really is doing a good job with Sebastian. Crazy brilliant Sebastian! Of course, John is getting some awesome help from his Lantean family and friends. And now John and Rodney are both determined to protect Sebastian’s interests – bring it. Anyone will regret f*cking with their boy. Thanks so much!

  9. Love the way you write John as a father. Actually just love this. And definitely wouldn’t mind if it ended up being 300K, :D

  10. Love love love

  11. I adore Sebastian.

    I adore this John and Rodney. (Yeah, I know. Such a surprise.)

    I adore this story. (Even less surprising…)

  12. Sebastian absolutely has a right to avoid Katie. And he’s also right about Rodney’s relationship with her – Rodney is being nice right now, but he’ll eat her alive eventually. Rodney shouldn’t have to hide his personality away, nor do I think he’d be able to long term. I like that Rodney is being a co-parent to Sebastian. However you take this fic (romantic or platonic), it’s already established that John and Rodney are close. They’re team. They’re FAMILY. Katie clearly doesn’t get that. I do love Sebastian asking women on the city if they’re single. And I bet he’s going to take the news that John is gay really well, and start thinking about what guys John could be with (though he’ll have to be more subtle because of DADT).

    I’m also glad that John is refusing to let Sebastian give up his intellectual rights to the ZPM theory, and that he knows Rodney wouldn’t allow him to do it either.

  13. I like this view of John, and I think that it could only be good for Sebastian to know that he has a fiercely protective guardian on his side.

  14. Thank you for your wonderful update! I love your John/Rodney/Sebastian interactions!

  15. Great chapter

  16. John is a good father.

  17. A thoughtful update shedding light on the conflicts to come. I dislike the whole idea of the IOA. Dr. Beckett just sounds so creepy and management is actually thinking of going ahead with his ideas. Thank you so much.

  18. greywolfthewanderer

    this is so fucking awesome I can’t even…


  19. Awesome chapter

  20. Personally, it doesn’t matter to me if it’s 30k or 300k, it will be John and Sebastian. That’s pure gold, and I’ll take it!


  21. OK, so, I’m loving this whole thing, but the whole thing with Rodney realizing that they were the aliens made me laugh. Why? Because when someone here in DK spouts off some Xenophobic BS I often laugh and say “Y’all are some of the oddest foreigners I’ve met yet.” The spluttering is epic because while they are busy pointing out how I’m a foreigner, they don’t realize that they are a foreigner to me. I usually just as “Are you from the US of A? No. Well then, that makes you a foreigner to me.” :D The sound of the kroner dropping is usually epic. LOL

    I love Sebastian!!! The kid is brill! Right… enough gushing, I gotta go read more. Toodle Pip!

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