Hello!
Well it's time for the final part of part 1, but don't worry - part 2 is on the way and will be posted here!
I was going to hold this chapter back for another day or two, but it was Scotland Comic Con this weekend (which was fantastic, and I got to meet Robert Picardo again!) and I managed to meet up with my Beta, The Mind of the Dragon, who read over this chapter recently and wants to know what happens next!
I don't honestly know what you'll all make of this chapter, but things are going to be getting pretty interesting!
Many thanks to VividVideoGeek, Forahr, Vadercat and Guest 64 for the reviews!
Disclaimer - I know virtually nothing about genetics, so apologies to anyone with a clue about them who reads this. For the record, the show doesn't have a good track record in understanding and/or explaining genetics either, so...
Atlantis, Lantea
Carson hadn't long finished taking blood samples from the Millers when he'd heard of the arrival of Lorne's team and the Athosians. He carefully placed the samples onto slides and labelled them before putting them into the Ancient sequencer. One the analysis began he tapped his headset.
"Beckett to McKay."
"Yeah Carson, what is it?"
"I'd like to know if you and the twins could make it by the infirmary before the festivities begin."
"Is there something wrong? Are they okay?"
"Your children are the picture of health Rodney, I'm just wanting to run some genetic tests in relation to your healing power episode. I can explain more when I see you."
"Sure, fine, give me five. They've only just woke up from a nap."
Five minutes later Rodney walked into the infirmary with Ewan stuck to his side and Elizabeth toddling in front of him, her father holding her hand as best he could.
"I really should have brought a stroller with me to the city...This is not doing my back any favours."
Carson chucked, "Have a seat Rodney."
Rodney manoeuvred to sit with a toddler on each knee. Ewan began staring around the infirmary while Elizabeth fixed her eyes on Beckett who smiled back at her.
"Sorry, she does that...the whole staring-at-people thing...How can we help you to help me?"
"Well..." Carson wasn't sure where to begin, "I came across a note on your medical file from the near-ascension incident which has in turn led me to look at some research the original Carson was carrying out at the time of his death. It was a project I had no idea existed, and it was near completion when the original Carson was killed, and I believe it's shed some light on how you were able to heal your niece."
"Is that good or bad?"
Carson fidgeted with his hands for a moment, "If the research pans out it won't be bad, and it won't be good...It will just 'be'."
"Don't ever quote me on this, but I don't follow you."
"Well you know how the only known indicator of certain Ancient ancestry is ATA-"
"-It's one of the main indicators, yes-"
"-It's the only one proven."
Rodney screwed up his face, "What do you mean? They're human. We're human. Surely you've done more research to find out how closely related the two species are."
Carson bit his lip and shook his head at his friend, "Surprisingly, no. Any other beliefs we may have had about how closely related our species were are hypothetical, and unproven. Or at least they were until I found my counterpart's research. What I've found from his research shows a few things – that there were at least two subspecies of Ancient and that they interacted differently with ATA technology from each other...And that your brush with healing powers was not a return to a state of near-ascension."
Rodney was quiet for a moment, and looked down at his two suspiciously well-behaved children before looking back up at his friend.
"It wasn't related to the ascension machine?"
"It still might have played a role."
"Okay...I don't say this very often so savour it – I'm a little bit confused."
Carson exhaled sharply, "I can only tell you the original Carson's theories. Nothing has been read or checked by my colleagues. Nothing has been peer-reviewed, but a map of your old genome created from a DNA sample you gave me before you were given the ATA innoculation supports what I believe."
"Which is?"
"The Ancients who came to Atlantis lived here long enough to become a separate subspecies of Ancient. While the original Ancient species utilised ATA technology, I believe that the Lantean subspecies further developed the technology. Samples of DNA in the database from the latter years of their time in Pegasus show the gene as always being on, and they interacted with the ATA technology in a far more profound way than either their forebears or we do.
"Ancients on Earth expressed the gene a little differently, and that's reflected in some of the oldest DNA samples in the city. Thank goodness the Ancients were so meticulous or the necessary samples wouldn't have survived. Some of the Ancients who first came to the city had the gene, but it was switched off."
"One of the things I do remember you telling me about ATA is that it's always on."
"Well I was wrong. It seems not all Ancients had the gene turned on by default, but after the first few hundred years, all the Ancients in this city had ATA switched on. Whether that was natural selection or genetic manipulation is anyone's guess. But ATA wasn't the only change."
"I get the impression you're leading up to some kind of bombshell."
"Perhaps...We know through mapping the genome of Homo Sapiens that you and I and every other human on earth share 99.9% of the same genes. But we also know that every human is genetically unique. We all have slightly different genes, some defective genes and some mutated genes. But patterns emerge among different sectors of the population."
Rodney nodded and Carson continued.
"When I examined your DNA I noticed that there were certain commonalities between your DNA and those of some of the earliest inhabitants of Atlantis."
"You're saying I might be descended from Ancients like Sheppard is? But I don't have ATA naturally."
"Well I might have slipped up there."
Rodney shot his doctor a look, "Oh well that instils confidence."
"Our test for ATA before the expedition started consisted of sitting people in the chair and looking for even the tiniest hint of a power fluctuation. The chair didn't even need to respond visibly for us to know if someone had activated ATA or not. For those we believed had no gene there was no response from the chair whatsoever."
"I remember that. You made me sit in the chair and then you told me that I didn't have the gene...But you didn't do any form of actual genetic test did you?"
"No," conceded Carson, "We thought the chair test was the most expedient way of doing it and it was approved by the IOA."
"I had the gene...It was just switched off, wasn't it," Rodney concluded for himself.
"Yes...The gene therapy only flipped the switch."
"I hate to say it Carson, but doesn't that render the gene therapy useless?"
"No...it just means that the success rate is a fraction of what we thought. We did successfully splice the gene into some people who did not have the gene either on or off."
"Hmm," Rodney quietened again, thinking some things over.
"So...I am descended from the Ancients."
"Yes."
"The main species...the ones that came to Atlantis millions of years ago."
"Yes...the individuals who didn't move to Pegasus, or die in the resulting plague, or learn to ascend stayed put in the Milky Way. And according to the archive they stayed in touch with Atlantis for a very long period of time. These were the Ancients that ended up seeding life on Earth and then sometime later – hopefully much later – must have interbred with our species."
"And Sheppard, with his ATA gene switched on?"
"Well I can't comment on individual cases but I'm sure you can fill in some blanks."
"He's either descended from far more modern Ancients, or directly from the evacuees that abandoned the city isn't he?"
"Aye."
"That must mean he has far more Ancient heritage than most people."
Carson nodded.
"That might also mean that he has enough Ancient DNA to set him apart from other humans."
Carson tried to give nothing away, but Rodney knew him too well.
"...He's more Ancient than Tau'ri, isn't he?"
"You cannot infer that."
"Or you'll be violating doctor-patient confidentiality, won't you?"
"You might infer that."
Rodney was silent for several seconds.
"It's not just him, is it?"
"I can tell you separate from his case that I have analysed my own DNA...I'll need to get my work reviewed by my peers...But it appears I'm slightly more Ancient than Tau'ri myself...such is the strength of Ancient genetics. They had far more varied genetics than we do...therefore a stronger genetic base, therefore they had more dominant traits that were passed down through the generations. For example, if there were two different genes - one Ancient, one Taur'i - that performed the same function, it would almost certainly be the Ancient one that would be passed down."
"As stunning as that discovery is...That still doesn't explain how I healed Madison," Rodney pointed out as Ewan reached to grab a pen from Carson's desk.
Carson gently prised the pen out of the boy's hand and continued to talk, "Thank you Ewan...You might be far more removed from the most modern of Ancients, but you still have far more in common genetically with the Ancients than someone with no ATA gene. You're not an Ancient, but by some standards you would certainly have enough Ancient genes to count as a hybrid of sorts."
"Um...Okay...Wasn't expecting that."
"We've also always hypothesised that Earth humans were programmed to follow the Ancients' evolutionary path, and many of the Ancients manifested near-ascension level powers long before they began to ascend. So it's been theorised that this evolution of abilities would eventually occur in Homo Sapiens as well.
"I believe that exposure to the ascension machine, coupled with your brain being forced to work with the chair link on a more involved level than normal, has forced or spurred your brain on to work in ways that might eventually have been expected of your descendants. I believe a combination of your own genetics, and your exposure to both the ascension machine and the chair link might have sparked an evolutionary change in you."
"But...I haven't manifested any other abilities, and I've not been able to heal anyone else."
Carson looked Rodney in the eye, "For now."
Stargate Command, Earth
It was safe to say John's return to Earth was not going as planned.
His expectations for today had been to leave the city early in the day, arrive at the SGC for a debriefing, and then to be assigned a security detail and be on his merry way to see his brother and arrange a meeting with his lawyer.
What had happened instead was worrying him deeply, and his stomach had slowly began to churn as the day had unfolded.
When he'd arrived in the gate room it had been oddly quiet, but he'd just come from the hubbub of the city so he'd figure his own perceptions might be off. Neither General Landry nor General O'Neill were present, instead he'd received an oddly cold glance from Colonel Mitchell before being guided to the SGC's infirmary where he's undergone a physical and some scans.
"We've updated mission protocols," Carolyn Lam had informed him, one of the few sentences she uttered during his stay in the infirmary.
After that ordeal he'd been told by Mitchell that he wasn't leaving the base and by this point Sheppard knew that something was up, and that arguing would get him nowhere. But rather than being led to guest quarters, he was taken instead to one of the SGC's secure interview rooms.
He'd been cooling his heels there now for several hours, the only interruptions being airmen arriving with his lunch, his dinner and the odd cup of coffee.
Every part of John told him there was something badly amiss, and for a while he wondered if an anomaly had sent him to a parallel universe or something, because stranger things had happened before.
His wondering would come to an end when someone would actually appear and talk to him.
As if reading his mind, there was suddenly some noise in the corridor outside, and the door to the interview room began to open.
"Speak of the devil," he murmured as General Landry walked into the room and took the seat opposite him.
"Hello Colonel."
"General."
Niceties over, Landry slapped a heavy file down on the table and started flipping through the pages at speed. John couldn't make out a word when Landry hit his own headset and instructed someone to begin recording.
"For the purposes of this recording this is September 14th 2012. I am General Henry "Hank" Landry."
John took the silent cue, "This is Colonel John Sheppard."
Hank was silent again, seemingly working out an angle for questioning. John had no idea what he'd done, but he had a feeling he was screwed.
"No idea why you're in here John?"
"Absolutely none Sir."
Hank nodded, grimacing, "There's two separate reasons actually."
Two? Oh he was royally screwed.
"Sir?"
"The first is regarding a Wraith transponder that was found in Atlantis as the attack began. The transponder was located by Technician Amelia Banks. She was questioned as per protocol before she was cleared for Atlantis, partly because we had not yet done a thorough analysis of the transponder.
"We've since completed a preliminary but quite telling analysis of the transponder. It appears to be have been in the city for quite some time. We believe even as far back as the Siege of Atlantis. For the entirety of the Atlantis expedition you were head of the military. Even the year that Colonel O'Neill led the expedition, she ceded control of the military to you. And while Atlantis has also always had a head of security, the safety of the city's inhabitants rested with you."
"Yes Sir."
"So how was that transponder missed?"
"I don't know Sir. It shouldn't have been. We ran sweeps after every skirmish, every incident, and every other week, with different people assigned different patrol areas for maximum effect."
Hank stared intently at Sheppard, "Evidently your patrols weren't effective enough."
"For that I can only apologise. I believed our procedures to be effective."
"That's not all. This apparent lapse almost cost us dearly. The transponder began to transmit as soon as the hives were in range. Wraith darts were over the Bay area almost from the beginning of the attack, but did not target any populated areas in the vicinity. They knew the city was there and started to fire on Atlantis as soon as she reached the surface. Atlantis was the vital component in the chair network and if it hadn't been for the effort in getting the city's shield up and running, Atlantis might not have survived, and without Atlantis we would not have known about the chair network in time. Your oversight, or lack thereof very nearly destroyed us all."
John swallowed, his insides churning over the details of Landry's frank assessment.
"For a senior officer this is an appalling failure of leadership."
"Yes Sir," it pained John to admit it, but Landry was correct.
"But we are open to considering extenuating circumstances – You were not the only senior officer to miss this. The head of Atlantis security from your second year on failed to spot the transponder, as did all of Dr. McKay's sciences teams. And the civilian leaders failed to carry out the appropriate checks and balances. It shows systemic top-down failures. So while ultimately the buck stops with you, you are far from the only person at fault. And that's why this discovery on its own wouldn't cost you your command."
John nodded solemnly, "Yes Sir."
Landry was quiet again, this time making some notes on a sheet in the file in front of him before continuing.
"However, I did advise that there are two reasons why you are in this room right now. Indeed it's closely tied to the reason you came back to Earth today."
"My son?" John's heart began thundering unhealthily in his chest at the inference.
"Partly."
"Is...Is he alright?"
"It would appear so, but we can't be 100% sure."
"What?" John felt his breathing become irregular and panic began to envelop him, "What do you mean 'we can't be sure'?"
"Your son has been removed from your ex-wife's care."
John couldn't think or a reason why they'd take his son off of Nancy, "Why? Where is he then? Is he with my brother and his wife?"
"No."
"Then?"
"He is in the care of a guardian appointed directly by the government."
"What?! Why? I need to know and I need to see him!"
"We can't do that," Landry's voice betrayed no emotion, "as there's an investigation underway."
"What kind of investigation?"
Landry was quiet.
"With all due respect Sir, this is my son! I deserve to know what's happening!"
"He's in care to undergo psychological observation for any sign of abnormal behaviour."
"He's not even two! He's a baby! What do you mean 'abnormal behaviour'?!"
"Colonel I'm going to need to ask you to calm down."
John flashed Landry as angry a look as he could muster before listening to the General.
"We need to do this with your son as a matter of security, and as for why do we need to this?"
"I don't know, 'sir', why don't you tell me?"
Landry gave John an unpleasant but mostly unreadable look that sent a deathly chill down John's spine.
"How the hell did you not know your ex-wife was a Goa'uld?"