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Author's Chapter Notes: As promised, my alternate take on “Aurora”, beginning with the group congregating in the control room after McKay announces his discovery of the “Aurora”’s signal


Disclaimer: I don’t own ‘Stargate Atlantis’ or any related concepts or characters; you know the drill by now. Also, the basic details of the plot were inspired by ‘The Phantom of the Opera’, although I have naturally put my own spin on things; hope it meets with your approval

Feedback: Always appreciated, trust me

Mystery of the Phantom


“What is it, Ro- Doctor McKay?” Elizabeth said, automatically amending what she was about to say as she noted Colonel Sumner standing off to one side of the control room; his recent near-transformation into an Iratus bug hybrid had almost made him more rigidly adhered to the command structure than he’d been before, as though he was trying to escape the memory of how rapidly he’d lost control by enforcing control where he could.

She was trying to encourage Sumner to talk to Heightmeyer about it- her recent conversation with Ronon and his comment about their differing methods of dealing with the Wraith had left her more than slightly concerned about the possibility of the Satedean leaving them, and the last thing she wanted was to give the man who was possibly their best ‘official’ fighter against the Wraith more reasons to leave due to disagreements with the commander-, but so far she wasn’t having much luck; the fact that his military duties hadn’t actually suffered as a result of his new attitude meant that she didn’t even have a valid reason for wanting him to attend the appointments.

That,” McKay replied, indicating a green dot on the main scanner screen behind him that appeared to bee sending the usual ‘ripples’ associated with the visual depiction of sound waves, “is the signature of an Ancient ship called the Aurora. With the ZedPM now powering the city, we've been reactivating dormant systems; that one tracked the location of Ancient ships during the war.”

“A warship?” Sumner asked briefly.

“Uh… yeah,” McKay confirmed, the brief gleam in his eyes suggesting that he’d been about to make a joke before he thought better of it (Another reason for Elizabeth not to like Sumner; he rarely seemed to allow people to be themselves), before he walked over to another, smaller screen. “Anyway, I cross-checked the logs. They were on a reconnaissance mission. When we activated the ZedPM, the city must have sent out some kind of an automated subspace beacon recalling ships back to Atlantis.”

“How long before it gets here?” Elizabeth asked; no matter what state it might be in after being abandoned for so long, the possibility of looking at an actual Ancient ship was incredible

“Well…” McKay said, as he turned around and began to type on the console below the screen, studying the information before him intently, “given that it’s at the edge of the Pegasus galaxy, let me see… carry the four…”

He shrugged dismissively as he turned around to look at the others. “Forty-two million years; should we go wait on the porch?”

“Alternatively,” Sumner said, his eyes narrowing as he studied McKay, “we could take a gateship through the nearest Stargate to check them out...”

“Unfortunately, as effective as that would be, there aren’t any Stargates in the area that we could use,” McKay said, his tone only slightly apologetic as he looked at Sumner, clearly enjoying being able to contradict Sumner in secure knowledge that the other man could say nothing to counter his claims.

“Which,” Elizabeth reflected as she looked over at the other members of staff in the room, “leaves us only one way to get there.”

She was just grateful that it was Daedalus’s supply week; the last thing she wanted was to have to wait for the ship to arrive when they had no way of knowing if the Wraith were going to be able to detect that signal just as they were...


A few hours later, with the Daedalus on route to the system where the Ancient ship had been detected- Sumner’s team had all insisted that they be allowed to go on the mission, even if Sumner himself had been content to leave it for Caldwell’s crew to handle until McKay had convinced him that their superior expertise with Ancient technology would be vital in such a valuable matter-, Elizabeth finally allowed herself to depart her office and head out to her balcony, passing off her destination to the rest of the staff in the control room as a need for fresh air.

As always, she barely had to wait for more than a few minutes before she heard a slight sound on the ground behind her, and knew that the man she was waiting for had come to visit her.

“You’re slipping,” she said, smiling nonchalantly as she turned to look at John as he stood behind her, a slight grin on his face under his mask. “I actually heard you that time...”

“Maybe I let you hear me,” John replied, as he walked over to take up a position beside her.

“Or maybe I’m just getting better?” Elizabeth countered nonchalantly.

“Either works for me,” John replied- Elizabeth couldn’t help but feel touched at that; for a man who spent his life trying to hide, the fact that he didn’t mind the possibility that she was aware of her was rather comforting-, leaning against the edge of the balcony before he turned back to look at her. “So, what prompted you to seek out this particular rendezvous?”

“The Ancient ship we recently discovered,” Elizabeth replied.

“Oh, that,” John said, nodding in understanding. “Well, it’s not that much-relatively speaking-, but I can assure you that I have no reason to believe there’s anything dangerous on the Aurora; I spent a bit of time reading some of the Ancient records of the last years of the war, and what I read about the ships from that area doesn’t suggest that there was any kind of viral research-”

“Viral research?” Elizabeth repeated, turning sharply to look at John. “The Ancients were experimenting with biological warfare?”

“I never found anything about them doing something like that in the records I read; I just said that because it’s the only thing the Ancients might have been experimenting with that could still be dangerous to people even after all this time if it was contained on a spaceship,” John explained, looking apologetically at her. “The point is, from what I could gather from the logs, there’s no reason to believe that the ship is anything other than an Ancient warship that ended up drifting around out there after the war ended; I just can’t give you any more information because I don’t have any.”

“I see,” Elizabeth said, nodding briefly at John before the two settled into a brief silence until she turned to look at him, hoping her discomfort wasn’t as obvious as she felt it was; this was the first time she’d ever asked him something on this topic, but at the same time she felt that it was time to try and broach this topic. “Actually, that brings up something else I wanted to ask you about; why... didn’t you investigate the Aurora yourself?”

John simply stood in silence for a moment, the expression on his face under his mask briefly leaving Elizabeth uncertain if he was going to answer the question or simply jump off the balcony and bring the conversation to a premature end, but then he finally nodded slightly- such a small gesture that she probably would have missed it if she’d had less experience at reading body language than she naturally possessed- and turned back to look at her.

“Well... I tended to limit how much equipment I activated in Atlantis to the things that I was certain I knew the functions of- and even then I only turned them on when I actually had some use for them; I wasn’t going to start wasting power on something when I couldn’t see a use for it and I needed to maintain the city shield while underwater-, so I didn’t actually know the Aurora was out there before you found it yourselves,” John explained, looking slightly uncomfortable as he spoke for reasons Elizabeth couldn’t entirely work out. “I read about it and a few other ships in the files, as I said, but I didn’t know it still existed; for all I knew it had been destroyed during the last days of the war...”

“I see,” Elizabeth said simply, noting another point in her private ‘file’ on John’s past; his knowledge of Ancient technology might be impressive, but it evidently was far from limitless. “So... what you know about Ancient technology, you learned through... trial and error?”

“And based on careful study of the Ancient language based on an initially basic knowledge of it; don’t forget that,” John said, his tone slightly jocular before his face almost appeared to close up as he processed what he’d just said.

“John-” Elizabeth began, curious for more information about his last statement

“Gotta go,” John said suddenly, hauling his feet up on to the balcony before he glanced back at her, his cloak hanging down around his body while his feet rested on the railing. “Good luck with the Aurora, Elizabeth; sorry I can’t be more help to you.”

“John-!” Elizabeth began again, only for John to leap out of view before she’d even finished the first word of her sentence, vanishing into the shadows of the city buildings around her before she could properly react.

Damnit... she thought to herself, hoping that she hadn’t pushed him too far with that last query; the last thing she wanted was to push John away when she still had so much more she wanted to learn from and about him. More than his Ancient knowledge- no matter how limited he apparently thought his knowledge of Ancient technology and language might be, what he’d displayed so far was definitely enough to impress her-, John himself represented a mystery she keenly wanted to explore, learning more about where he’d come from and the events that had shaped him into the man he was...

She just wished she knew why those details were so interesting to her; was it just because knowledge of the Phantom’s past might encourage the SGC to be more open to the possibility of future collaboration with him, or did she want to know simply because she wanted to know?

The more she learned about John, the more she found herself uncertain why she wanted to know these facts in the first place...


As he walked through the silent corridors of the Aurora- he’d ordered the team to split up and search the area independently after life support had been activated; the general lack of active life readings made it fairly clear that the ship was safe-, Sumner was starting to feel increasingly uncomfortable with the current mission; as if their earlier close call with that Wraith ship hadn’t been enough of a complication- they might have easily destroyed it, but one Wraith ship could easily lead to more if they weren’t lucky-, when you added in the fact that there were a bunch of Ancients being kept in stasis pods on a ship where they’d only just managed to reactive the life support systems a few minutes ago, he was starting to feel increasingly like he was on a ghost ship from classic gothic fiction...

He wasn’t sure if he felt better or worse now that life support was back up and running; the spacesuit might have offered a certain extra degree of protection, but that didn’t totally compensate for the restricted movement and fundamentally enhanced combat vulnerability it offered (Particularly when the Wraith’s abilities in airless environments were unknown; there was still some debate about how long the Wraith could last without oxygen or how they might cope in an airless environment).

So far, however, this entire trip was rapidly beginning to seem like the greatest waste of time since their trip to Dagan only to learn that the ‘Phantom’ had already taken the ZPM that the Ancients had left there for himself; the ship was a wreck, the crew were nearly dead, there was no way to know if there was actually anything useful in its databanks...

Colonel Sumner?” McKay’s voice suddenly said over his radio, drawing his thoughts back to the present.

“Yes?” he answered briefly.

I’ve just completed my scanning of the stasis pods, and... well, I’m reading cortical signals!” McKay replied, in an enthusiastic tone that meant nothing to Sumner.

“Which means?” he asked, hoping that whatever had made McKay so excited would at least go some way towards making this trip worth the effort.

Basically, the pods have all been equipped with neural interfaces indicating brain activity as though the Ancients were fully conscious,” McKay explained. “If all of these pods are interconnected, it's highly possible these people are, in fact, communicating with each other.”

Sumner blinked.

There was no way he’d just heard that correctly...

“Are you saying... these Ancients have been talking to each other via some... mental network... ever since they went into stasis?” he said incredulously. “But... wouldn’t that have been at the end of the war?”

Well, it would have been an effective means of keeping their minds occupied until they were rescued, but what I’m seeing suggests that the interface was only reactivated when they detected the recall beacon from Atlantis,” McKay explained. “Anyway, the neural feedback loop is incredibly active.”

“Is there any way that we can find out what they’re saying in there?” Sumner asked, hoping that he was right and McKay actually had a reason for bringing this discovery to his attention in the first place; the concept of the neural network was interesting, but it didn’t actually serve much of a practical purpose on its own.

Well, that’s what I really called you about,” McKay answered. “We found a couple of empty stasis pods that we could use to link one of us up to the network, but I... well, I thought you’d prefer it if we updated you on the situation before we did anything...”

“Good call,” Sumner said, as he turned around and walked towards the area where he’d previously sent McKay. “Get everything set up; I’m going in there.”

He might not be the most scientifically-based member of his team, but he was the team leader; if they were going to make contact with Ancients, it was his responsibility to do so.


“Hold on; you want to do this?” McKay said, looking incredulously at Sumner.

“As team leader, part of my responsibilities do include officially making contact with the worlds and people we visit; the potential importance of this encounter makes adhering to that procedure all the more vital,” Sumner pointed out, folding his arms as he glared at McKay. “The fact that you’re volunteering to go into that network yourself confirms that it’s safe to access; leaving you out here is simply practical sense in case something happens that nobody was expecting.”

“It won’t!” McKay said in protest.

“But if it does-” Sumner pointed out; looking back, he had to admit that it was a rare occasion when a plan based on McKay’s scientific expertise ended up going completely according to plan.

“It won’t!” McKay protested, his apparent traditional fear of danger pushed aside in favour of defending his scientific expertise. “How many times do I have to say this?!”

“Rodney,” Teyla added, in her usual diplomatic tone- for a woman from a relatively primitive society Sumner was often impressed at how well she’d fallen into her unofficial role as their ‘liaison officer’ for some of the less advanced societies they’d discovered-, “between the two of you, if something were to go wrong, which would be the greater loss?”

“Well,” McKay said after a moment’s pause, apparently missing the glare Sumner shot Teyla as she stared nonchalantly back at him, “I’ve never thought of it that way, but...”

He glanced over at Sumner. “She’s right; you should go.”

If it wasn’t for the fact that her ‘deception’ had allowed him to get what he’d been after in the first place, Sumner would have made a mental note to have a talk with Teyla and McKay about undermining his authority while in potentially hostile territory; as it was, he simply handed his excess gear to Ronon and laid down in the pod that McKay had just opened for him.

“Assuming I decide to leave, how does that feature work?” he asked, glancing at the Ancients lying in the pods around him; he’d read enough reports about encounters with brain-manipulating technology that had been encountered back in the Milky Way galaxy to know that he couldn’t be too careful.

“Well, it’s simple enough, really,” McKay explained in the manner that always left Sumner feeling like McKay thought he’d just asked the equivalent of how to fit the cubes into the holes on a child’s toy. “Once you’re plugged in, the system creates a direct feedback loop between the processor and your brainwaves, so when you want to disconnect, you just need to... well, concentrate.”

“In other words, when I want to get out I have to think about getting out,” Sumner stated briefly.

“Well, you’d probably need to specifically think about it in order to prevent yourself from popping in and out every time it crosses your mind, but otherwise... yeah, you’ve got it,” McKay said, nodding briefly at the colonel before he indicated the control console in his hands. “Now, I should be able to monitor your EEG patterns, so in the highly unlikely event that something anomalous should present itself, I should be able to, uh, disconnect you manually-”

“Good,” Sumner said as he laid back in the pod, looking briefly and pointedly at McKay as he waved a prompting hand. “Let’s get on with this.”

“OK,” McKay said, swallowing slightly in the face of Sumner’s glare as he moved to stand alongside the pod. “Now, when I close the lid, the pod system should activate. Ready?”

“I’ve been ready for the past few minutes, Doctor McKay,” Sumner said, looking over at the scientist in frustration. “Just get on with it.”

“Uh... good,” McKay said, tapping on his laptop and sending the pod back into its ‘booth’, leaving him, Teyla and Ronon looking silently at the now-seemingly-unconscious colonel as he entered the virtual environment.

“Well,” Ronon said after a moment’s silence, glancing back over at Teyla and McKay, “since that’s done, better get back to work; still got a lot of this thing to search.”

McKay wasn’t sure what struck him as more depressing; the fact that Teyla and Ronon were so quick to abandon Sumner to lie around in a pod where he might not even be able to accomplish what he’d set out to try and achieve, or the fact that he himself was only sticking around because he didn’t want to have to deal with the arguments he’d have to put up with if it became public that he’d left his team leader behind.

In the end, it was pretty much what he’d said to Elizabeth during that whole crisis with Sumner mutating into a bug; he just couldn’t bring himself to feel that bothered about Sumner beyond a professional capacity. Elizabeth and Carson had been good friends even before they’d arrived there, Teyla was fairly easy to talk to once you got on a comfortable topic for both parties- she tended to just walk away when he talked to her about stuff, but some of her insights into the cultures they’d just visited were rather interesting-, and even Ronon wasn’t that bad- the man might not really socialise with people that much, but at least he gave the impression that he might miss you if you died-, but Sumner actively seemed to avoid anything that wasn’t involved with training or preparing for the next mission or going over how you’d screwed up on the last one...

Quite frankly, McKay was starting to realise just why Carter, Jackson and O’Neill had gone to such extreme lengths to get Teal’c back; if you were going out into the unknown wonders of the galaxy, you felt more comfortable to have someone at your back that you knew would save your life because they wanted to do it, rather than just someone who was there to do the job.

Shaking those self-analytical thoughts aside, McKay sat down against the pod, laptop in one hand and gun in the other in case the situation turned ugly, and waited for something to happen.


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