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Primum Movens, Part II, CH III

<<< Back to Primum Movens, Part II, CH II


She was lost in the dark. 

Elizabeth tried to move but something was holding her in place.  The darkness was complete; blinding and giving no hint of where she was or when she was.  

For a split second she thought she might finally have been condemned to the fate she was expecting, that the Replicators had won.  But her last memories were of being safe and contained in Atlantis.  She had no recollection of why that might have changed. 

The room began to illuminate and a subtle murmur grew clearer.  Voices.  A number of them.  She swallowed uncomfortably as a table lit up and faces emerged from the dark, dressed in white and studying the center of the table with interested—or distrusting—eyes. 

Elizabeth spoke to a thin, blue-eyed man seated in one of the chairs.  He did not respond.  He could not hear her.  

He turned to a woman to his left, one with glossy black hair and a peaceful, if reserved, expression.  Elizabeth recognized her from a recording she’d seen in the first days of the expedition.  The library program. 

No.  Her name is Melia. 

She suddenly realized she knew them.  Melia.  Janus.  Moros.  The Ancient Council.  Just as her alternate timeline persona had known them.  Almost all of them with faces Elizabeth recognized and knew as well as she knew her own expedition members, though she had no idea how. 

One of the council rose, a portly gentleman with snow-white hair.  Elizabeth knew him, too—a scientist, by the name of Pygalmous. 

“I presume you all know why I have called this meeting of the Council,” he began, gesturing towards the area at the center of the table.  “So far, we have made some impressive progress with the nanorobots.  But at this time, it is nowhere near what we hoped to achieve.” 

The remainder of the Council glanced to where he was pointing.  Elizabeth followed their eyes to a tube, one that looked similar to the tubes used to contain the nanovirus when they’d first discovered it in the labs in Atlantis. 

It dawned on her what it was she was seeing.  A scene from the past.   The visualization of a memory. 

Like with the whales. 

So real she felt as though she could speak to them.  But this memory happened thousands of years ago. 

“I should say not,” a female Ancient was saying, who Elizabeth only vaguely recognized.  There was a slight quirk to her smile.  “What they are is aggressive, uncontrollable little monsters.” 

“You would do well to keep your unfounded opinions to yourself, Pandora,” said Moros sharply.  The Ancient’s smile faded, though her eyes continued to display her amusement.  

“She is not incorrect—the nanorobots are still quite aggressive,” said Pygalmous.  “But as that was the primary purpose for creating them, I do not regard it as a failure.” 

“Indeed, from what I understand, the nanorobots are rather effective weapons as they are,” said Janus.  Elizabeth studied him with interest, this thin, soft-spoken man who would become so kind to her alternate sometime in his future. 

He leaned back a little in his chair, his voice increasing in volume as he continued.  “You have ensured they cannot harm their makers with your genetic restriction.  So I do not understand your concern.  As they are, they appear to be swift and efficient in their method of destruction.” 

“And that is where the problem lies.  They are too swift and efficient,” answered Pygalmous.  “They exist right now at a basic level, no more adept than a virus—and no more able to discern their victims.  We have managed to prevent them from attacking us, yes, but only because we share a common genetic trait.  For other races who do not possess that trait, the nanorobots pose a threat that will be difficult to control.   We cannot find genetic commonalities between every single sentient being in the galaxy that are not Wraith.  And there is not enough data about the Wraith themselves to let us know whether such a protocol would work in the reverse.  We simply have no way to ensure the nanorobots will attack only that which we would prefer they attack.” 

“What do you propose, Pygalmous?” asked Moros, his face set in a severe grimace.  “How can we correct this problem?” 

“I would like to introduce the nanites to a more advanced system and attempt to program them not to destroy that system, but rather, to learn from it.  To learn from it and develop a construct similar to it—one much more advanced, that would afford them the opportunity to learn how to single out the Wraith.” 

“What type of an advanced system are you referring to?” questioned Janus. 

Pygalmous did not answer immediately.  It took the remainder of the Council only a moment to deduce what he was not saying.  

Melia turned to him with a horrified expression.  “You cannot be suggesting we allow the nanorobots to try and copy our genetic code?” 

“That is a very risky endeavor, Pygalmous,” said Janus.  “Allowing machines to copy the genetics of living individuals is a gigantic evolutionary step.” 

“It is nothing of the sort,” replied Pygalmous.  “Should the experiment prove successful, all we would have created is a much more advanced machine, with programming that will be much more easy to manipulate and control as we see fit.” 

“I do not understand why this end cannot be accomplished by our own programming,” said Janus.  “Why not do this manually as you have been doing?  Why the impatience?” 

“Impatience?”  For the first time, Pygalmous displayed emotion beyond the carefully controlled expression he’d been wearing for his presentation.  “You have seen what has happened with the Wraith in the last few years.  Do you really believe we have the time to waste with impossible experiments?” 

Moros eyed the scientist calmly.  “Our scientists have made great strides, which you yourself have overseen.  Why do you now deem it impossible?” 

Pygalmous folded his hands, taking a breath, resuming his calm demeanor.  “It is not that I believe them incapable.  But we have barely managed success with our nanorobots in a block formation, and those creations are extremely simplistic.  What we need here, what we do not have, is the time to develop the more complicated programming these creations need in order to be effective, discerning weapons.  To do so we must program them on the level of freethinking beings.  The difference genetically between one of us and a virus similar to what the nanorobots are now is, as you well know, extreme.  To program them to equal our level of development will take an extraordinary amount of time—years.  Decades.  It may be impossible.  We will have wasted thousands of hours on a weapon which we cannot employ at all.” 

“And yet you are basing your entire request on a hypothesis,” said Pandora, her arm draped casually on the table.  “You have no guarantee the nanites will even be able to read a living organism.” 

Pygalmous turned to Moros.  “Given how the nanites react when introduced to an organic structure and how they were able to be prevented from harming us, I believe it is completely possible to program them to assimilate an organic structure.” 

“Assimilate?” questioned Melia.  “How would this work?” 

“We would introduce the nanites to such a structure and allow them to hybridize it at a cellular level.” 

“As you have been doing now?  Using tissue samples?” 

At this question, Pygalmous’s demeanor shifted to uncertainty.  “The tissue samples are not enough.  The nanites destroy them because, despite containing a complete genetic blueprint, they are not part of a working whole.  I believe they need to be introduced to a completely functioning structure in order to understand the components—seeing how the genetic components work to create physical unification.” 

Janus studied him seriously.  “Are you suggesting allowing the nanites to assimilate a living person?” 

“It could mean death,” said Melia, with wide eyes.  “If they acted as aggressively as they do now, they could destroy every cell as they copied it.  No one could survive such a process.” 

Pygalmous glanced at the large vial.  His voice sounded distant, detached.  “If we are to attempt to make them into an efficient weapon against the Wraith, it is a risk we must take.” 

“I take it you have already found a volunteer for this measure?” asked Moros.  His expression had not changed, even with the most surprising of Pygalmous’s revelations.  He seemed almost unfeeling—which matched completely what Elizabeth knew of him. 

“There is a man—a Commander of one of our ships—whose family was killed during one of the Wraith’s last assaults.  He has volunteered.” 

“Does he understand it could mean his life?”   Asked Melia.  

 “His entire family was tortured and murdered.  As far as he is concerned, he no longer has anything worth living for.” 

“If we were to approve this—” began Moros. 

“Moros—” interrupted Melia, with a surprised expression. 

The leader of the Council held up his hand.  “If we were to approve it—would we be able to control them?” 

“They would be computer programs, nothing more,” said Pygalmous, “subject to our commands and our control.” 

“Your control?  You cannot control them now,” interrupted Pandora.  “Let’s not forget the nanites do not obey commands at the level they are—“ 

“Their simplicity is their problem, as I have said,” answered Pygalmous.  “By introducing complexity to their systems, we can shape them into creations which will serve us exactly as we need them to.  Once we have the coding, we can alter it to suit our needs.”  

The Council was silent.  

Janus looked at Pygalmous after a moment.  “How do you plan on enacting this experiment?” 

“I have developed a machine which will study and store the assimilation data within it,” Pygalmous said.  “A capsule that can allow the assimilation to occur safely.” 

“And if it succeeds?”  Asked Janus.  “What then?” 

“I will have to analyze what data the nanites build from the assimilation.  But if they develop a construct similar to what I theorize they will, then we can move to the programming stages and start building more complicated structures.  There is a list of planets in the database rich in the material we need.” 

“I still do not agree with this,” Melia said, swallowing and staring at the seemingly empty vial.  “It seems hasty.” 

“Nothing is hasty when it concerns the Wraith,” answered Moros.  “I agree with Pygalmous.  If he is ready, begin.  At this point, we do not have much left to lose.” 

The Council rose.  

Janus turned to leave, then looked back at Pygalmous, who was reaching for the vial.  “Just out of curiosity—who is this volunteer you speak of?  This captain willing to give his life?” 

The elderly man paused.  “His name is Oberoth.” 

The remainder of the Council walked out, some with set faces, some with frowns.  Pygalmous reached once more for the vial.  As his hands closed over it, a beeping sound filled the room and the world disappeared in a snap.  




Elizabeth sat up, her eyes widening.  Around her, machines were beeping recklessly and Jennifer Keller stood over her, her face set with a grim look.   

“Welcome back, Elizabeth,” she said, rather matter-of-factly.  “You scared us for a minute.” 

“What?”  Elizabeth raised a hand to her head.  Her hair was damp with perspiration, as was her clothing.  “What happened?” 

“You collapsed in the isolation room,” John said, moving in from the shadows.  They were in the infirmary containment area, where he, Keller and Woolsey were standing.  

“You had a seizure,” Jennifer remarked.  She grabbed a penlight from her tray and shone it in Elizabeth’s left eye.  “I need you to lay back and relax for me.” 

“What caused it?” 

“Not sure,” John said.  “We were talking and then you just collapsed.” 

A quick glance between him and Woolsey told her a lot more than his explanation, and reminded her of the options he’d told her she had as far as the IOA and SGC were concerned.  A sudden, unexplained seizure did not bode well. 

“I think…I think I jumped into a memory.  Or an observation,” she said finally.  Jennifer pressed on her shoulders, and she reluctantly lowered herself to the bed.  John and Woolsey moved forward to crowd the edge.  “It was about Janus.” 

“Janus?”  John asked, a frown on his face.  “ As in ’Ancient scientist’ Janus?  The one the other you met?”  He cocked his head to the side.  “Not the replicator you, the other other you, you know, the old version?” 

“Keller looked over at him.  “Old version?” 

“Yes,” Elizabeth cut the inquiry off sharply, throwing John an exasperated look.  “That Janus.” 

“What’s that Janus doing in your head?” 

Elizabeth shook her head slowly.  “I have no idea.  But it wasn’t just him.  The entire Ancient Council was there.” 

“The Ancient Council?  Why were you having visions of them?” asked Woolsey cautiously, as though he was afraid to upset her.  Or rather, upset Keller, who regarded him with a slightly irritated expression. 

“I’m not sure.  I walked into them having a discussion,” she replied.  “About the nanites.  Or what we would call the nanites.  They called them nanorobots.  They were discussing—I don’t know—ways to improve them.” 

“Improve them? 

“Yes.  Apparently they were like—” She glanced over at John.  “They were still like they were when we first discovered them here.  Like a virus.” 

“You mean a plague,” John replied, crossing his arms. 

“That was the scientist’s concern.  That he couldn’t get them beyond that stage.  At least not quickly.  So he was asking permission for assimilation.” 

John’s lips pursed, and he threw a quick look at Woolsey.  As calmly as he could, Richard asked, “They were figuring out how to make the nanites assimilate?  A human?” 

She looked up at him, her eyes wide.  “I think so.  I think they may have used human DNA as model for the nanites’ programming.” 

“But Niam told us the Replicators created themselves,” John said cautiously. 

“Niam only said that the nanites eventually bonded and created the Replicator race on Asuras.  He never said what the Ancients did to make them capable of advancing to that level, though,” Elizabeth said.  “If what I saw was correct, then scientist wanted to use human cells as a sort of blueprint.  But the intention was to create more intelligent nanites, not human form replicators.  Somehow something must have gone wrong.”  

“Hmm.  An Ancient experiment going wrong.”  John crossed his arms.  “Imagine that.” 

“Well, replicating human DNA isn’t exactly simplistic,” Jennifer was injecting something into the IV above Elizabeth’s head.  She paused, glancing over at them.  “If the nanites succeeded in assimilating the cells, which we have to assume they did, chances are they became too complicated for the Ancients to control.  The ones Rodney used to heal your cells replaced them with almost perfect nanite copies.  And they were far too advanced for him to completely control what they could do—though I don’t think I have to explain that to you.” 

Elizabeth smiled wryly, then yawned.  

“So, they assumed they could control them,” John said.  “Just like The Matrix.  Without, you know, the cool leather jackets.” 

“But why take such a risk is my question,” said Richard.  “It seems reckless, especially considering what they did help create.”  

“I don’t think they felt they had a choice.  At least, that’s the argument the scientist and Moros made,” Elizabeth said.  “They needed the nanites to be a weapon against the Wraith, and it was taking them too long to figure it out.  They were desperate.” 

“It’s basically the same reason Rodney had to go back to the FRAN model,” Jennifer said.  “He didn’t have time to figure out a basic structure and build from scratch, so he had to use human-form replicator programming to create FRAN to speed things up.” 

“And that worked out so well,” scoffed John. 

Elizabeth shook her head, suddenly feeling drowsy.  “The scientist said—he said the volunteer was Oberoth.” 

“Oberoth?  As in Asuran-evil-leader-and-master-of-the-Collective Oberoth?”  John asked. 

A warm, fuzzy feeling was overtaking Elizabeth in waves, and she struggled to keep her eyes open.  But after a moment, she managed a nod.  “I guess so.” 

“He was a human.”  John had his eyes narrowed. 

“A commander of some kind.  He lost his family to the Wraith.  I think it was his DNA they copied,” she continued, before another yawn stopped her.   Keller motioned at the men to leave the room.  Richard backed away reluctantly.  John turned to follow, but Elizabeth threw a hand out, grasping his arm.  “John, I need to speak with Rodney.” 


“The Ancients mentioned there was a list of planets…” 

John’s voice sounded far away.  “Planets?” 

“With neutronium cores.  I think it might be in my nanites’—” 

His face blurred into a mixture of dull colors before fading to black. 




“You think it was a nanite induced memory?”  Richard asked. 

“It’s the only logical explanation,” said Rodney.  Sheppard had called the scientist and Keller up to Woolsey’s office for a conference on Elizabeth and what steps to take next. 

“We know Elizabeth was nowhere near a conference of the Ancients—not our Elizabeth, anyway.  So how else would she remember a meeting with the Council?” 

“She made it up?  It was falsely planted in her head by her evil twin?” said John.  “Take your pick.” 

“Based on what you said she said, it seems way too complicated to be something she made up,” Rodney said.  “But if the nanites were programmed with the Atlantis system, they may have records and data about conferences and other things the Ancients were involved with.  I mean, she listed facts we can check, right?  Like Oberoth being a Commander.  The Ancients might have scrubbed all mention of the Replicators from the database, but I’m guessing they didn’t delete all the ships logs.  There should be mentioned of a human Oberoth somewhere in them.  If there is, I’m betting that Franibeth would not have had access to that information.” 

“Will you stop calling her that!” said John.  

“What?  It fits doesn’t it?” Rodney said, continuing on before Sheppard could answer him.  “In any case, if what she’s saying is true, we might be able to hook her up—” 

“No,” Richard started, but Rodney held up a hand. 

“Hook her up like we did Frani…like we did the Replicator, to an isolated system, and dig through the code to find the answer.” 

“No,” said Jennifer. 

The men turned to her where she stood, arms crossed.  

“No?” squeaked Rodney.  Jennifer turned to him with, if Richard had to describe it, a rather scary expression on her face. 

“Whatever you may be thinking you can gather from her, she is still a person, not a machine,” she said, her tone brooking no argument.  “The effect of this last memory, or whatever it was, was equal to a seizure.  Probing her mind might lead to a more severe reaction.” 

“Like how severe?” asked Rodney tentatively. 

“Like it might kill her,” answered Jennifer matter-of-factly.  She turned to Richard.  “Whatever you want to try and argue about her status with the IOA or the SGC or even these two, for my part, I don’t really care.  As the chief medic, I’m committed to keeping the person she is alive.  I won’t condone any more experiments on her until I know what effect they might have on her physical, HUMAN system.” 

Rodney’s eyes were the size of saucers, and even Sheppard looked a little intimidated.  

“Are we clear?  Good.”  Jennifer looked at Richard.  “I’ll be in the infirmary, with my patient.” 

She walked off, and Richard glanced at his head of science and head of military ops with a surprised look.  “Well.” 

“Jennifer’s just tired,” said Rodney sheepishly.  “She’s been really busy with all the, you know, stuff that happened.” 

“Remind me to bring ‘tired Keller’ along the next time I come face to face with a Wraith Queen,” John remarked.  “She’d give Teyla a run for her money.” 


“Whatever Doctor Keller’s concerns, I’m afraid they might not be as pressing as the information you seem to think Elizabeth can provide,” Woolsey replied.  “If she does indeed have a list of neutronium rich planets in her head somewhere—“ 

“We could use them to find where the Replicators are hiding,” finished John.  

“It may be of the utmost importance we get our hands on that list,” said Richard gravely. 

Rodney nodded.  

“I think Elizabeth would agree with you,” John said, looking resigned.  “No matter what the cost.”




Teyla held up the picture of Torren and Kanaan, taken most recently on New Athos, towards Elizabeth, who grinned broadly.  “What a handsome pair.” 

“I would not disagree,” she replied with a smile.  “And this is when he was newly born.  I believe John told you what happened.” 

Elizabeth nodded, taking the other picture from her, her brow knitted in concern.  “Had I known how much trouble Michael would cause you I would never have sanctioned that experiment to begin with.” 

“There are many things we may regret as far as our choices are concerned,” said Teyla.  “But I have learned, very recently, that for all the wrong choices we feel we may have made, we should regret nothing.  All were made for a reason.  And while some may have led to pain, there was also much joy to be found.” 

She looked back down at the picture.  “I have Torren, and I have Kanaan.  Michael is gone.  And in a way, his interest in my people, even if it were based partly on revenge, may have preserved them from the Wraith.  For all this, I am grateful.” 

“I like the way you think, Teyla,” Elizabeth said. 

Teyla reached into the box, pulling, for the second time in as many weeks, an Athosian clay pot from its contents.  Elizabeth’s eyes widened at the sight of it.  

“I believe this was a gift,” Teyla said. 

Elizabeth took the pot into her hands.  She was unable to speak for a few moments, and when she did, her voice came out as a whisper.  

“Thank you, Teyla.  For keeping this safe.” 

“I can put it away until you are able—” 

“No.  I think it’d like to keep it here,” Elizabeth said.  “It has so many good memories tied to it.”  She studied the pot, the smile dropping from her face.  “You know that the Elizabeth we met that first year—the one that had gone back in time—she met them.  Janus, and Moros.  The Council of Atlantis.” 

“I remember.” 

“I didn’t really know what they looked like, other than what the SGC has on file for them and what we had in our database.  Now, I know exactly what she saw.  They’re so clear to me now.” 

“You are certain you were really seeing them?” 

“I don’t have any doubt.”  Elizabeth furrowed her brow, thinking.  “What concerns me is how I have that knowledge.  They’re obviously not in my memories.  Where did they come from?  Or more importantly, who put them there?” 

“Your nanites contain a great deal of information, Elizabeth.  It is entirely possible that instance was part of it.” 

“That’s what concerns me.”  She placed the pot on her lap, casting her gaze down.  “Programming can be manipulated.  What if that is what this was?  A manipulation, put there by the Replicator when she attacked me?” 

Teyla sighed.  She felt as though this question was one that would always permeate her discussions with Elizabeth, and even John, where Elizabeth’s nanites were concerned.  She laid her box of memories aside and reached a hand over to her friend, clasping the cold fingers tightly. 

“I know you are concerned for the well-being of Atlantis.  But please, Elizabeth, for this moment, remember that you are, for all intents and purposes, you.  If there is something to be concerned about, trust that the people of Atlantis will find a way to handle it when the time comes.  But at the moment, in this moment, you are simply Elizabeth Weir.  My friend and someone I am very grateful to have this time with again.”  

Elizabeth was silent for a few seconds, but she laid her other hand upon Teyla’s and squeezed.  

The door to the isolation room slid open, and Mr. Woolsey entered, followed by John and a very irate looking Jennifer Keller. 

“Doctor Weir,” said Mr. Woolsey, glancing from her to Teyla then back to Elizabeth.  “We have something to ask you.”




Elizabeth studied the schematics of the stasis pod, marveling at the advancements made in such a short time since her capture.  The look of them was different and seemed much more efficient than what she remembered. 

Jennifer was over by the monitoring equipment, triple checking everything and occasionally throwing a dirty look towards the trio of Rodney, John and Richard, who were trying as inconspicuously as possible to appear as though it didn’t bother them and failing miserably at it.  Especially Rodney, who made puppy dog eyes every time Jennifer’s back was turned. 

Rodney and Keller.  Who would have thought? 

Carson was assisting Jennifer.  It had apparently been his hand who had worked this system with the Replicator version of her, though as Jennifer pointed out, her stasis would be different because she was human and not replicator. 

It had been the lead-in to the host of other problems Jennifer foresaw happening from this little experiment, but Elizabeth agreed with Richard and John—if she had a list of neutronium laden planets hidden somewhere in her head, they needed to find it as soon as possible.  It might be the only way to catch the Replicators before they did whatever it was they were planning. 

“How are we coming?” she asked, shoving her hands into the pockets of her black pants.  Teyla had managed to find her a black t-shirt, so she was no longer conflicting with Richard’s wardrobe. 

“Almost done,” said Rodney, with a jump and a squeak as Keller directed another look at him. 

The young doctor turned to her, her expression softening.  “Doctor Weir, I know you feel like you’re up to this, but I really think…” 

“It’s no use, love,” said Carson, with a half smile.  “You’re not going to change her mind.” 

“Listen to the man,” said Elizabeth.  “He knows what he’s talking about.” 

“Only because I’ve been around the block with your stubbornness a few times or so,” Carson replied.  

“Still—” Jennifer started, but Elizabeth walked over to her and placed a hand on her shoulder.  

“I understand your concern, I truly do.”  She smiled.  “But right now, there is something more important than just my life at stake.  We have to find out where those Replicators have gone, and I’m willing to risk anything for that.  I hope you can understand why.” 

Jennifer frowned but patted the hand resting on her shoulder.  “First sign of any serious trouble and I’m pulling you.” 

Elizabeth squeezed her shoulder, then glanced over at the guys.  “Gentlemen?” 

“Just waiting on—” 

The door to the lab slid open and Zelenka, followed by Ronon, squeezed by the Marines stationed at the entrance.  “I have it here.  Everything I could cross compare to what we know of neutronium planets in this galaxy.” 

“That should be a good starting point,” said McKay.  “If you want to…”  He gestured with his hand towards the stasis pod, and she nodded, and moved into the container. 

As Rodney punched on a few buttons, she looked over at the Satedan.  “Hello, Ronon.” 

He nodded in response. 

She looked toward John and lifted her eyebrows, with a smile, at Ronon’s demeanor.  

“Yeah, some things never change,” he quipped, as Ronon moved up beside him. 

“Okay, we’re ready.”  Rodney stopped and looked over at her with wide eyes.  “Are you sure you’re ready?” 

She gave him a comforting look.  “As ready as I’ll ever be, I suppose.” 

“We’ll be monitoring you carefully,” said Carson.  “Don’t worry about a thing.” 

“With you guys in charge?  Did I ever?”  She said.  The response was a series of quiet chuckles around the room. 

She closed her eyes to the sound, and in a flash, the room and everyone in it was gone. 




Jennifer kept an eye on the monitor before her, which showed Elizabeth’s heart rate at a steady, normal rhythm.  

She looked over at Carson, who presented her with a reassuring smile.  “No worries.” 

She took a breath and returned her focus on the monitor.




Ronon tilted his head as McKay tapped a command onto his computer tablet.  In the stasis pod Weir was still, her eyes closed.  She looked peaceful.  Very different from the open eyes of the Replicator when they’d tried it with her.  

Sheppard adjusted his stance, his hands resting casually on his P-90.  He showed no emotion, but his eyes had not looked away from Weir or the scientists since she’d stepped in the thing.  Whether it was because he’d learned his lesson or not Ronon wasn’t sure, but his interest was completely different than it had been when the other one was here.




John studied the sleeping form of Elizabeth, still not quite processing the weirdness of it all.  It was like déjà vu wrapped up in a really bad dream wrapped up in an alternate universe.  Hard to look away, kind of like watching disaster flicks. 

“Ta!” Rodney said and started doing the quick-tap thing on his tablet.  

“Find something?” Zelenka asked.  

“The search I’m running pulled up something matching in her nanites’ code.  Hold on—yes.  Looks like some kind of coordinates—” 

The heart monitor started to beep more quickly.  Keller jumped on it, her eyes flickering towards Rodney but saying nothing. 

“Hurry it up,” John whispered to the scientists.  Rodney eyed him with irritation, but at his gesture towards Elizabeth, nodded in reply. 




“These,” said Pygalmous, his hand waving over a holographic map of a portion of the Pegasus galaxy.  He and Janus were the only two within the room.  “Three here and there are three more in quadrant two.” 

“And they are out of sight of any Wraith planets?” Janus questioned. 

“As far as we can tell.  The Wraith are spreading quickly, but as there are no human colonized settlements in these areas, they have very little to interest them here.” 

“How are the nanites reacting, Pygalmous?” asked Janus, as the hologram disappeared.  “Have they shown any development since the assimilation?” 

“Development?”  Pygalmous smiled.  “They are developing at an exponential rate.  The programming they created is overwhelming.  It is all we can do to keep up.”  

“So then it has worked?” 

“Until we have a creation we can control, I will not know for certain.  But at this rate, we will have an intelligent, functioning mechanism within weeks.” 

“And there is no danger of them becoming uncontrollable?” 

“The nanorobots will always be a danger so long as we are programming them to be weapons.  There will always be a risk,” answered Pygalmous.  “However, it appears that the non-attack protocol I programmed into the advanced nanites carries over into their new evolutions.  They will not attack us unless that protocol is altered.” 

“And can we ensure that protocol will not be altered?” 

Pygalmous stared at Janus with a slightly condescending expression.  “Of course, I wrote the programming to inhibit them from reprogramming themselves.  Only if one of us were to alter it would it change.” 

“I understand.  I am simply attempting to ensure we do not create the same problem with them as was created with the Wraith.” 

“Provided we do not possess the same arrogance about these creations as those who created the Wraith did, we should be sufficiently protected.” 

Janus did not look convinced, but he said no more.  

Elizabeth studied the hologram, then glanced about the rest of the room in curiosity.  

She froze as her eyes fell on a form in the far corner.  Watching from the shadows was a pair of bright green eyes, set in a pale face, and framed with jet black hair. 

Her Replicator form moved from the corner out into the brightness of the lab.  Janus and Pygalmous paid her no notice.  Elizabeth shook her head and turned and fled the room.




Carson checked the stasis pod readings as Elizabeth’s EKG started spiking.  Her brain wave activity was very heightened, certainly not even close to average for someone who was supposed to be in deep stasis.  

He would feel a great deal better if he could wake her. 

“How much longer, Rodney?” he asked.  McKay waved a hand at him, his eyes excitedly scanning over the code running across his tablet. 

“Give me another five minutes,” he said.  Jennifer was staring knives into his back, but he didn’t seem to notice. 

She looked at Carson, the irritation dissolving into concern.  He tried to keep his reaction a little less obvious, but he did need Rodney to hurry. 




Rodney was barely able to process the results from the expanded search he was running as it came through the computers.  He was delving into portions of Elizabeth’s nanites’ programming he’d never gone through before.  In a way, they were very similar to Franibeth’s, with the same seemingly extraneous coding actually containing a wealth of information.  It seemed impossible something so small could harbor so much—and yet, they were capable of assimilating, assembling and were truly artificially intelligent, so why would he doubt? 

They’d gotten a handful of planets meeting the criteria for replicator building early in the scans, but Rodney had wanted to take it a little further just to make sure he wasn’t missing anything.  There wasn’t time to go through even a fraction of what the programming contained, but if there was anything about the Primus they needed to know, he wanted to find it before it found them. 

Somewhere behind him the monitors were beeping incessantly.  If there were a problem, Jennifer would alert him, but for now his focus needed to be right where it was at—in the science. 




The dark, quiet room was familiar.  It wasn’t Atlantis; it wasn’t Ancient.  

Where had she seen it before? 

There was a pod there, one that looked archaic.  In a flash, she remembered. 

The Primus capsule. 

It was in pristine condition, looking untouched and unused.  Set in the same location she’d seen it before—when John and the others had found her. 

But why was she here now? 

She reached out for it, touching the cool, ancient surface, and closed her eyes. 




John turned as the heart monitor attached to the stasis capsule began beeping much more quickly.  Jennifer turned to Rodney.  “Her heart rate is pushing one hundred and sixty five beats per minute.  It’s too close.” 

Rodney glanced up at her, his eyes half glazed over from reading through the code.  “What?” 

“This is too taxing.  She’s still weak from the last seizure, you can’t push her this hard.” 

Rodney frowned. 

“Do you have what you need, Rodney?”  Asked Carson. 

“Uh…not…quite?” he murmured softly.  John knew that expression.  It more than likely meant that he did, but that he’d stumbled onto something more interesting. 

“What is it?” John asked. 

Rodney turned to him.  “She has some data here on the Primus.” 

“Primus?” asked Jennifer.  “I thought you were looking for that list of planets?” 

“I am.  But we know the Primus is tied to it somehow!” 

“Is it really that important?  We already know she’s Elizabeth!” 

“Important?!”  Rodney looked back at her in indignation.  “Of course it’s important!  Everything having to do with the Primus is important!” 

John fidgeted with his P-90.  “How much more can she take?”  

Carson shook his head.  “Maybe another minute, maybe a little more.” 

“Maybe a little less,” said Keller. 

“Hurry,” John replied, this time aimed at Rodney.  McKay wasted no time.  At Jennifer’s perturbed expression, John nodded towards the pod.  “Elizabeth would want him to try.” 

Keller’s mouth quirked a little, but she knew enough of Elizabeth to know he was right. 




Oberoth, as she remembered from Asuras, was before her.   He was standing across from Pygalmous, his expression neutral.  The scientist had his hands behind his back, but in his eyes there was fear. 

“It’s gone too far,” Pygalmous said.  

“Too far?” Questioned Oberoth.  “What do you mean?  Have we not done as you instructed us to do?” 

“Yes.  What you have built here…” the Ancient trailed off, his eyes gazing about the room before returning to Oberoth.  “It is fantastic.  More than I expected you would be able to do.  You evolved much faster and to a much greater extent than I ever imagined.  But what you have begun doing—the modifications you have made—they are too much.  The Council perceives them as such.” 

“You see us as a threat,” replied Oberoth emotionlessly. 

“The Council does.” 

“You created us,” Oberoth said.  “Your Council approved our measures.  We cannot hurt you.  What logical purpose does it serve to destroy us?” 

“They do not like what they cannot control,” Pygalmous said.  “You have gone too far.  Building your own versions of yourselves, creating a society—” 

“We did not go too far,” Oberoth replied.  “We created the most efficient system.  You have put in protocols, limited our abilities—” 

“I have tried to make every argument I can to the Council.  But you must understand, you were never supposed to become this complex to begin with.  When you copied Oberoth’s form, the Council became alarmed.” 

The Asuran Oberoth frowned slightly.  “His DNA was what we were instructed to assimilate.  Naturally, his genetics would be the basis for our first attempts at a complex system.” 

“But you must logically understand that creating forms that are identical to living beings—alive or dead—poses a problem.” 

“You have programmed within us the protocol that forbids our copying any sentient organisms in the future.   This will not happen again, so I fail to see where the Council should be concerned.” 

“You have evolved well beyond our control, Oberoth.  Your city, your system—it is not something we commanded you to do.  The Council has already condemned the usage of nanite programming in androids for fear of what it might cause.  This…evolution…you have engaged in makes that development appear miniscule by comparison.” 

“Based on the data we were able to gather during the assimilation, anything less complex than this form would not be able to perform as you wished.  A life form lower than human form would be base in comparison.  We would not be able to discern the distinctions between the Wraith and any other type of being unless we were capable of recognizing them through our own conscious awareness.  As we are now, we can discern what is most logical—what it is you wish of us, as a race of beings.” 

“But you are not a race of beings,” Pygalmous said.  “You are machines.  Your programming may one day be overwritten.  The Council does not wish to take the chance that it may happen when you are thousands strong and could threaten us all.” 

Oberoth continued to stare, unbending and seemingly unfeeling.  “So you will destroy us.” 

Pygalmous lifted a hand.  “I am sorry, Oberoth.  But we no longer have a choice.” 

“Considerate, were they not?” said a cool voice from the shadows, interrupting the memory.  “The Ancients.” 

Elizabeth whirled around.  The Replicator form of her was standing in the far corner of the room, also observing the memory.  “Thankfully, they were also not very bright, despite their intelligence.” 

Explosions sounded around them.  Pygalmous jumped, surprise written across his face.  

“It appears we are not the only threat to the Council,” Oberoth said remorselessly. 

“They would not,” said Pygalmous softly.  “They would not dare.” 

“Your ideas brought them to this point,” said Oberoth.  “It is wholly logical that they would want to eliminate all chance of this threat recurring again.  That must include the mind responsible for its origin.” 

Pygalmous moved to the window, where Ancient ships were beginning to populate the sky.  

“They may destroy these forms,” said Oberoth.  “But unlike you, it takes only a few of us to survive.  And we still have the capsule.” 

“Where is it?”  As Pygalmous turned, he clasped his hands behind his back, his expression becoming extremely calm. 

“Safe,” replied Oberoth.  “If it is needed, it can be used again.” 

“You cannot use it,” said Pygalmous.  

“It is only a matter of time before we find someone who can.” 

Elizabeth looked back to the Replicator of herself, who smiled.  

“So it was,” she said.  

The room burst into an explosion of white-gold light, and Pygalmous, the Primus Capsule and everything around them dissolved away.




The monitors were beeping wildly.  Rodney glanced up at John, wide-eyed.  “I can’t pull her out of it.  Something’s gone wrong!” 

John glanced over at the pod, his pulse quickening as Keller and Carson moved to find some way to control the spikes in Elizabeth’s heart rate and blood pressure.  Even Ronon looked concerned, his eyes on Elizabeth’s frozen form, his fingers tapping his forearm in a barely perceptible motion. 

“Figure it out,” John said, moving to stand beside Rodney.  “NOW!”




Elizabeth was in a dark hall, one she was unfamiliar with.  Her feet were pounding across the tile floor, colored in the style of the Ancients.  Bubble lamps glistened around her. 

Where she was headed and where she had come from, she did not know.  She only knew she needed to get somewhere, quickly. 

The hall brightened before her, and as she reached the entranceway it opened up into a massive Gateroom.  Only, unlike the one in Atlantis, this gateroom had no walls or ceiling.  It opened up into the darkness of space, with a plethora of stars hanging overhead, and the Gate, at the end of the long tile floor, stationed in the middle of it.  

She raced towards the shining pool, feeling the need to jump through it.  Soft footsteps followed her, and she turned at the wormhole to see the replicator Rodney had made moving towards her.   

She took two more steps towards the pool, a hand reaching out towards it, only she felt compelled to look once more.  As she did, the empty room was gone, and she was looking at the faces of Richard, Rodney, Ronon and Teyla. 

And John.  John, who turned away from her. 

She turned to a group of unfamiliar Ancients behind her. 

No—not Ancients.  Replicators. 

Don’t worry.  I’ll go first. 

John met her gaze one last time, his expression careworn.  She smiled reassuringly at him, her hair falling against her shoulder, then turned and walked through the Gate. 

She felt the wormhole release her as she stepped through.  She’d known where she was going.  She knew it wasn’t where the Replicators following her were expecting. 

Her eyes opened and the Gateroom was gone.  Only the Gate remained, slowly ushering in the other Replicators who had followed her through, whose faces showed surprise and despair at her trickery. 

She felt her eyes close.  She felt the cold.  But it did not disappear, not the world around her.  It was still there.  Her movement was slowing, her thoughts, her anxieties, growing smoother, but the world chased around in her mind, unceasing, and unable to be stilled. 

She was going to be here, like this, no sound, no sleep, no life.  Nothing. 






Keller’s voice broke across the blackness.  Warm hands were on her skin, a cool surface beneath.  

“Elizabeth?  Elizabeth!” 

That was Carson. 

Her eyes flew open.  Monitors around her were beeping like crazy.  She blinked, her heart thrumming in her chest so quickly she could barely feel it beat. 

She couldn’t breathe.  

Her chest constricted, and Jennifer was in front of her, placing a steadying hand on her forehead.  “Breathe.  Calm down, Elizabeth.  Calm down and breathe.” 

Her eyes darted to the scenes around the room.  Everything had stopped; Rodney’s hands were poised above the computers he’d been using, his eyes wide, his expression concerned.  Richard had a fist to his lips.  

“Elizabeth,” Carson was at her other ear, and he smiled kindly as she turned to him, her throat feeling tight and her head beginning to ache.  “Come on, dear.  Take a breath.” 

A hand found her shoulder, and she looked up into the brown eyes of Ronon, who knelt at her side.  John stood above him, his lips a tight white line, eyes locked to hers. 

He didn’t need to say what he was thinking.  

Come on.  Breathe. 

Ronon’s hand squeezed. 

Her chest released, and she shuddered and coughed as the cool air burst across her dry throat.  She took a breath, and another, as Carson’s smile broadened.  “Good girl.” 

John’s footsteps sounded heavy as he stomped away.  He stopped near Rodney.  “What the hell was that?” 

Rodney opened his mouth to answer but he had nothing.  Jennifer was looking at him too, her eyes narrowed, and he shrugged, turning back to the computers.  

“It’s…it was my fault,” she gasped.  Jennifer’s expression melted into concern. 

“Don’t try to talk.  Just relax for me, okay?” 

“Did you get it?” Elizabeth asked, looking at Rodney. 

Rodney looked guiltily over at her.  “The…” 

“The list of planets,” she said, gulping in another breath. 

“I think we did,” he said softly.  “Look, Elizabeth…” 

“It was my fault,” she repeated, firmly this time.  She looked over at John, who was still staring at Rodney in anger.  “I went looking for it.” 

“Looking for what?”  He asked.  “What was so damn important you’d risk your life for it?” 

“The Primus.  I wanted to find out what it was they wanted.” 

“Who?” asked Carson. 

“Altus.  And…and the other one.  The other me.” 

“Not.  You,” John barked. 

She met his gaze but said nothing.  After a moment, she looked over to Richard.  “I think I know what it was they needed me for.  And how Oberoth was involved.”




Rodney clicked a button and flipped his datapad around.  “It was a ship called the Telum.” 

Telum?”  Woolsey’s face creased into a confused frown.  

Rodney glanced back down at the list.  “According to the Ancient Database, it was captained by a Commander named Oberoth.  An Oberoth who suddenly disappeared off the logs.”  

“So he was alive,” said Ronon. 

Sheppard, seated across from him in the conference room, leaned back in his chair.  “Anything else?” 

“No.”  Rodney shook his head.  “They more than likely purged his records after, you know, he sort of became robot fodder.” 

“Is that what happened?” asked Richard.  “He was assimilated into a replicator?” 

“I don’t think so.”  The group turned as Elizabeth entered, looking much better than when they’d pulled her from the stasis pod.  Rodney’s eyes flickered towards Jennifer, who trailed Elizabeth along with Teyla and a pair of Marines.  Upon noticing Sheppard, they nodded and set up position outside the doors of the conference room. 

Elizabeth walked over to one of the chairs, sliding into it easily.  Teyla moved over towards Ronon and Jennifer took the seat next to her, her eyes looking everywhere around the room except at Rodney. 

He swallowed and tried to ignore the tight feeling in his chest.  

“What do you mean?” asked Woolsey, looking at Weir.  She glanced first at him, then towards John.  

“I think Oberoth sacrificed himself to their experiments, but he wasn’t assimilated.  He was killed during the assimilation.  But since his DNA was what they analyzed, his form was the first one the nanites took when they became human-form.  That’s why we met an Oberoth when we visited Asuras.” 

“Basically, they copied him,” said John.  “Like a blueprint.” 

Elizabeth nodded.  “The fact they did that is the reason why they were prevented from taking human form again, as Niam explained to us.  But the Oberoth we encountered wasn’t Oberoth the Ancient.  He was the first human-form replicator—the result of the Primus experiment.” 

“Primus experiment?” 

She nodded.  “The capsule—what you found me in?  That was what Pygalmous used for the assimilation.  It was built like a stasis pod, for the human component.  But its purpose was to record the nanite activity.  To keep record of it and all the data the nanites collected.” 

Rodney thought for a moment.  “So they used that stasis pod like a research computer?” 

“I think so, yes.”  Elizabeth said, sitting back. 

“So, then…” Rodney sat up, an idea suddenly occurring to him.  “That capsule contained all the original data—everything the nanites learned from the human Oberoth!  And, and…”  He snapped his fingers, his thoughts spinning almost too quickly to articulate.  

“Saved it,” John finished, his expression stoic.  

“Saved what?” asked Woolsey. 

“The programming,” Sheppard replied, his eyes flashing with displeasure.  “The original experimental programming that guy—Pig-whoever—was trying to cobble together.” 

“The pure code,” Rodney breathed. 

Teyla glanced between them.  “What does that mean, exactly?” 

“It means that code was untouched—not tampered with,” Elizabeth said.  “What the Primus capsule contained were all the building blocks the nanites used to eventually create human form replicators.” 

“And that information was saved in the capsule?” asked Jennifer. 

Elizabeth turned to her, nodding.  “It was part of what I saw.  Oberoth—the Asuran version, the one we met—mentioned they had the capsule stored away somewhere safe.  The Ancients were destroying Asuras, trying to get rid of the replicators, at the time.   To protect the Primus capsule, Oberoth had it hidden away, so they could use it again, if they needed to do so.” 

“So why didn’t they?”  Jennifer’s expression was twisted in a pert, cute wrinkle of confusion.  Rodney felt his chest tighten again.  “If all they needed to do was reset their code, why didn’t they just use the capsule to do that?” 

“Pygalmous wasn’t a fool,” Elizabeth replied.  “He was the one who programmed all those preventative protocols in the nanites to prevent them from harming the Ancients, from taking human form, and so on.  My guess is he built the same requirements into the Primus capsule.” 

“Making it so a replicator couldn’t use it,” Richard replied.  

“A replicator couldn’t.  But a human could,” said John, staring directly at Elizabeth. 

“Yes,” she replied quietly, nodding.  “I think that was Oberoth’s intention when he put me in there.” 

“Yes, but if he could not use the Primus, then what good would it do him to place you inside?” asked Teyla.  “If he was unable to activate it?” 

“All he had to do was wait,” said Elizabeth firmly.  “He could not activate it, but he knew who could.” 

Woolsey was looking between them confusedly.  Rodney understood, as did Sheppard, exactly what she was implying.  As Woolsey’s gaze fell to him, Rodney sat back, his heart sinking into his chest.  “She means someone with the Ancient gene.” 

John’s expression was the same, though his mouth curled down into a frown.  “We set it off.” 

“More accurately, I did,” Rodney said.  He was afraid to look at Jennifer, but when he chanced at glance at her, she was, strangely enough, looking at him with soft eyes. 

Elizabeth smiled sadly at him.  “My guess is, when Rodney touched the Primus pod, it activated the transmission.  That was why Altus needed you to find me first.  He couldn’t make it work—” 

“But we could,” finished Richard. 

“But if that was the case, wouldn’t you have just been assimilated?” asked Jennifer.  “Why didn’t it do to you what it did to the ‘real’ Oberoth?” 

“That I don’t know.  Maybe that was the intention.  Or perhaps the control I exercised over the nanites in my system prevented the programming in the capsule from doing what it had done before.” 

“Sharing information with you instead.”  Rodney said.  “You absorbed it but you didn’t get affected by it.” 

“Wait.  I thought you said you checked her out and that she was good,” said John, looking at Rodney, an edge to his tone.   “Wouldn’t you have noticed the difference in her nanites when you examined her?” 

“As I have said repeatedly, there are literally billions of lines of code in Elizabeth’s nanites,” Rodney snapped back, more harshly than he intended.  “It’s possible I missed a few here and there.” 

“A few?  If this thing worked with the replicators’ original base code wouldn’t that be more than just a few?” 

“Depends on what they affected.  And considering that Elizabeth remained in control, its possible she affected what they did.” 

John cocked his head.  “So basically what you’re saying is that you have no way to know exactly what the hell it is they did do.” 

Rodney opened his mouth, then thought better of arguing.  “No.” 

“So if I’m understanding all this correctly,” said Woolsey, “What Altus and Frani…er, Elizabeth’s Replicator copy wanted was this original programming, which was transferred to Elizabeth when you brought her out of stasis?” 

“More or less,” murmured Rodney. 

“When she probed my mind, she was trying to get her hands on that Primus programming,” said Elizabeth.  “That has to be it.” 

“Why would they want it?” asked Richard. 

“Because it’s not a Rodney special,” said John.  

At Richard’s quizzical expression, Rodney splayed his hands.  “The programming they stole from Elizabeth should, presumably, have very little limitation on it—none of the modifications I’d have made on either Altus or FRAN.  With it, they could get around the preventative protocols in their code right now.” 

“So they go back to how Pygalmous originally programmed them,” Woolsey said.  “But even in that case, at least based on what Doctor Weir has related, they should still have some basic limitations in them.  Even Pygalmous wasn’t foolish enough to let them start from scratch.  He transferred some safety protocols into the pod before the nanites began processing, right?” 

“Well…”  Rodney murmured, squinting a bit. 

“Well?” asked Teyla, with a frown. 

“There is the added problem of the fact that Altus was one of those replicators who was hooked up to the Asuran Collective when I programmed in the back door the first time we visited.  And maybe even when we reactivated the attack protocol on our second go around.”  He looked at Elizabeth, who closed her eyes, as if to confirm what he suspected. 

“Meaning what?” asked John. 

“Meaning he may have the keys in his own code to override even the Ancients’ security protocols.  So to speak,” he replied timidly. 

“Hold on.  Let me get this straight,” said John, his voice tinged with anger.  “Between what they stole from Elizabeth and what they already had thanks to your tinkering, they basically have the ability to write themselves into whatever form they’d like to be, with no limitation?  Carte Blanche, replicator style?" 

“Uh, sort of.  Essentially.” 

“Essentially.” John crossed his arms, narrowing his eyes at Rodney. 

“So if they do this format and reboot,” Ronon began, then furrowed his brow as Woolsey threw him a surprised look.  “What?  I’ve been on Atlantis four years, I can work a computer.” 

Elizabeth smiled wryly at him.  

“Anyways, should they reset themselves, how long would it take to replicate?”  The Satedan continued. 

“It would take them a while to get everything prepped to begin replicating.  My guess is they’d rebuild the City structures, labs and everything before they begin to recreate themselves, so we may have some time.  But how much?  I could only make an educated guess,” said Rodney.  “Maybe a few weeks.” 

“And after that?” asked Teyla.

“The one thing I'm pretty sure they won't alter in their programming is that attack protocol.  It seems to be the one thing they really enjoyed doing,” answered John.  “They'll pick up their war on the Wraith where they left off, like we thought they would, and anything in their way be damned.” 

“Doubly so, with unlimited capabilities. Basically, we’ve helped them unlocked the potential to release replicator Armageddon on the galaxy,” Richard summed up.  The room went silent and Rodney swallowed, feeling more guilt than he had in a long, long time.  And recently he had a lot to feel guilty about. 

“So what kept you clean?” asked John, after a minute of silence.  His expression was serious, but there wasn’t exactly suspicion in his eyes as he watched Elizabeth.  “You saw all of this because your Replicator swapped programming with you.  Are you sure you aren’t compromised?” 

Her response was equally as serious.  “I can’t answer that with any kind of assurance, but I think that whatever control I’ve been able to exercise over my nanites prevented them from controlling me completely.  In fact, I think we might actually have swapped information, for lack of a better term.  I took some of her programming when she tried to copy mine.  Regardless, I know one thing for certain.  This is my fault.”  Elizabeth bowed her head.  “I should never have let you bring me here.” 

John shook his head.  “You had no choice.” 

“But I—” 

“We’re all to blame,” said Richard authoritatively.  “Had we not poked the hornet’s nest that was Asuras to begin with, none of this would have happened and so on and so on.  We can walk around in circles trying to figure out where it went more wrong than not, but that’s beside the point now.  The only thing that matters is finding a way to stop it before it starts again. 

“Doctor McKay?”  Woolsey rose, gathering his papers.  “Keep on that list of planets, and find us some suitable options.  We need to find whatever it is they’re planning and destroy them before they get the chance to finish.” 

“What if we’re too late?”  asked Rodney. 

Richard’s expression was deadly serious.  “We should pray that’s not the case, Doctor.  Because if it’s too late for us, then it’s too late for this entire galaxy.  That is the one thing we can be absolutely certain about.” 


>>> Continue to Primum Movens, Part II, CH IV

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