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Author's Chapter Notes: 1: Thanks to Infinite Freedom for suggesting the name of the F-302 pilot I used here
2: Hope you guys like my new resolution for the F-302 crisis; it wasn’t easy to think up, but I like to think I came up with something plausible

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

An hour later, as Sumner stood on the Daedalus’s bridge staring at the computer screen above him, displaying a language that he’d only seen briefly and already knew he’d seen enough of to last him a lifetime, he couldn’t help but curse.

“We have a Wraith computer virus in our systems?” he said, looking critically over at McKay and Caldwell, uncertain who to berate first; this might be Caldwell’s ship, but McKay was the alleged ‘genius’. “How did we miss this earlier?”

“In all likelihood it was transmitted in a compressed format during our battle with them,” McKay explained. “It probably took a while to reach a point where it could spread to the point where it could affect our systems; we wouldn’t have noticed it during the initial check of the computer systems after the battle, and it probably only activated after some kind of trigger event.”

“What kind of ‘trigger event’?” Sumner asked.

“Possibly the fact that we’re once again in close proximity to Wraith territory?” McKay said, looking over at the colonel with an anxious expression that did little to truly express how terrified the current situation must be making McKay feel. “From what I’ve translated so far, I think it was ultimately designed to take control of the navigational system; fly the ship right to them.”

Sumner didn’t need to be a scientist to realise the implications of the Wraith getting their hands on the Daedalus; with access to the information in the Daedalus’s computers, they’d not only learn Earth’s coordinates, but they’d also have access to information about how to duplicate the intergalactic hyperdrive technology that Earth had acquired from the Asgard…

“Hold on,” Sumner said, looking pointedly at McKay as a thought occurred to him. “I understand why the Wraith would have installed this virus, but that doesn’t answer why someone on this ship would kill Lindstrom and Monroe…”

His voice trailed off as an obvious suspect suddenly occurred to him. “Hold on… are you saying…?”

“It was the virus,” McKay confirmed. “It’s actually simultaneously an elaborate artificial intelligence; it can think for itself, adapt itself to new situation…”

“And protect itself by eliminating anyone who might find out about it,” Sumner concluded.

“Can it take over the whole ship?” Elizabeth asked.

“Not entirely,” McKay replied, indicating a couple of monitors nearby. “You have to remember that there are hundreds of individual computers on board. A lot of them are interconnected so we tend to think of them as one big machine but that's not really the case. There are dozens of back-ups and redundancies, and some systems – like life support – are deliberately isolated.”

“So, you’re saying that we don’t have to worry about losing our atmosphere,” Sumner replied, even if he doubted the virus would go that far; the Wraith would almost certainly want to feed on them after going to so much effort to acquire the ship, even if they kept some alive to interrogate.

“There’s that, but you have to take into account that some of the more complex systems like navigation and propulsion require a certain amount of interconnectivity to function properly,” McKay continued, almost automatically dampening the brief flare of hope Sumner had felt. “In all likelihood, the virus has spread so far through those systems that to isolate it will make the ship impossible to fly. Until we figure out how to get rid of it, we're stuck here.”

Before Sumner could ask for further elaboration, an alarm suddenly started to beep from another part of the control room, prompting the small group to look over at one of the lieutenants.

“Sirs…” the lieutenant said as he looked uncertainly at Sumner and Caldwell- although Sumner deferred to Caldwell’s authority, many of the military were still sometimes uncertain who to acknowledge first-, “we just… began broadcasting a distress call.”

“What are you talking about?” Caldwell asked, walking over to look at another monitor.

“It just came on by itself, sir,” the lieutenant protested. “I’m trying to shut it down, but I’m locked out.”

“It’s the virus,” McKay said, prompting Caldwell and Sumner to look back at him. “That's what I mean about adapting itself to new situations. It doesn't have enough control yet to fly us to the Wraith so instead it's calling the Wraith to us… and right now, we are sitting ducks.”

Damnit… Sumner growled, shaking his head in frustration.

There were some days when it was not worth getting up.

An hour or so later, Sumner’s already-low opinion of the current situation had only decreased. Although McKay had managed to come up with a means of eliminating the virus by shutting down and rebooting the system, that had still left them with the issue of the transmitter array, until Captain Chris Price- one of the Daedalus crew, assigned to the ship after displaying a particular knack for understanding the F-302 operating systems- had suggested the most direct manner of dealing with the problem; destroy the transmitter array in an F-302, which he had just taken out of the Daedalus hanger in order to put his plan into action.

“All right, Captain,” Caldwell said, going over the latest report one last time as he addressed Price’s F-302 over the comms system, “we've evacuated all sections in the vicinity of the array and sealed the bulkheads.”

Understood,” Price replied simply, his voice betraying none of the anxiety he must have been feeling at this time.

“All personnel,” Caldwell added, tapping the necessary buttons to redirect the radio to address the rest of the ship, “brace for impact.”

For a moment there was nothing, and then the ship shuddered under a sudden impact that stopped before it could really start.

“What’s our status?” Caldwell asked, glancing over at another lieutenant.

“Transmitter is offline,” the lieutenant confirmed, shooting a relieved smile in Caldwell’s direction. “Distress signal has been disabled.”

As McKay and Weir exchanged relieved looks, Caldwell reached over to activate the radio.

“Well done, captain,” he said over the radio link, apparently nonchalant about how close they’d come to destruction. “Return to the ship.”

With pleasure,” Price replied, only to speak again a few seconds later with an uncertain tone. “Uh… we have a problem; my controls aren’t responding.”

“Say again?” Caldwell asked.

Well,” Price said, clearly trying to stay calm, “I’m currently moving further and further away from Daedalus at an alarming speed, and I can’t seem to turn around…”

“Oh no…” McKay said, looking over at the others in horror. “I should have seen this coming. The navigational software on the F-302 is compatible with our sublight system, which has already been infected; the virus must have uploaded itself onto his ship.”

“Can we transport him out?” Sumner asked.

“That should work; those systems are still clean…” McKay said, turning to face his console before a voice suddenly cut in over the radio.

OK, Daedalus, don’t get too worried; I think I’ve got an idea here,” Price said, his voice sounding remarkable calm for the current situation. “The navigation computer’s the only problem; if I can shut down the engine and take the computer offline, I should be able to get back to you without any problems…”

“What?” McKay said, hurrying over to activate the radio in response. “Captain Price, don’t do that; you’ll trigger the virus-”

I’m taking the computer off-line, Doctor McKay; the virus can’t do anything-” Price began.

“And you think that thing isn’t prepared for something like that?” McKay countered. “This isn’t like on Daedalus; we can isolate it over here, but-”

The sound of an explosion over the radio was suddenly cut off as the radio dissolved into static, leaving the bridge crew staring solemnly around at each other before Sumner broke the silence.

“What just happened?” he asked, turning to look critically at McKay.

“Well…” McKay said, looking around with an uncertainty that suggested he was expecting to be blamed for this, “basically, Captain Price must have assumed that he could shut the F-302’s systems down and remove the navigation computer so that he could navigate back to us manually… but, given that it takes a few minutes for him to shut everything down, the virus must have realised what he was doing and triggered the self-destruct to stop him getting back.”

“The virus did that?” Sumner said, looking sceptically at the Canadian scientist. “I thought you said this thing was an artificial intelligence programmed to deliver us to the Wraith; why would it want to blow Price up?”

“Maybe it figured that Price had shown he’d be more trouble than he was worth and thought that a death like that would demoralise us; I’m a programmer, not a psychologist, how am I meant to know how a homicidal virus thinks?” McKay protested, before he sighed and turned back to the console before him. “Anyway, on a somewhat more encouraging note, we can safely shut down the virus’s access to the ship’s self-destruct systems before we progress with trying to wipe the system here; the F-302 was just quicker because there were less computers for the virus to access for it to get its job done…”

“Forget the explanations,” Sumner said, turning to glare at McKay. “A man is dead, Doctor; if you can stop any more of us dying, do it now.”

A couple of hours later, as McKay went over the last of the computer files necessary to be backed up and restored, he couldn’t stop thinking about Price’s death; as much as he might have liked to attribute the other man’s death to his own mistake, he couldn’t deny that the plan could have worked under normal circumstances, but he’d been unable to give Price all the information about what they were actually dealing with- Sumner had ruled that it would be ‘demoralising’ to know they were up against an AI of this scale and simply attributed their issues to a computer virus that caused malfunctions-, and so Price had taken what seemed like the ‘logical’ course of action without knowing everything he needed to know…

As he completed the last back-up, McKay pushed those thoughts aside; recrimination wasn’t going to help anything now.

“Alright, colonel,” he said, activating his earpiece radio to put him back in contact with Caldwell, “we’re ready!”

Thank you,” Caldwell’s voice said, before the radio shifted to allow the colonel to address the entire ship. “All personnel, this is Colonel Caldwell. Prepare for a full system shutdown.”

After a moment’s pause to allow everyone to stop whatever they were doing, Caldwell spoke again. “All right, doctor, go ahead.”

Nodding in confirmation, McKay nodded at Hermiod, the Asgard activating the controls on his own console, plunging the ship into darkness for a few moments before he reactivated the systems, the ship lighting up as though nothing had happened.

Engine room,” Caldwell’s voice said, “what’s our status?”

“All systems are functioning normally,” McKay confirmed with a relieved smile. “No sign of the virus; looks like it worked, Colonel.”

“May I suggest we vacate this system? Our current position may well have been compromised.”

Can you give me hyperdrive?” Caldwell asked

“That will take longer to get back online,” the Asgard replied with his race’s usual neutral tone.

“I can get you sublight,” McKay added, looking at Hermiod as though he wanted to be sure the Asgard recognised that he’d just accomplished something useful before flicking a switch.

For a moment, as he felt the ship begin to move around him once again, McKay almost allowed himself a moment to believe that all was going well…

Then he studied the information on the screen before him, and realised that that was far from being the case.

Damnit!” he yelled, hurrying over to check Hermiod’s console to re-confirm his findings before hurrying back to his own.

Engine room,” Caldwell said over the radio, “what’s happening?”

“The virus; it’s back!” McKay answered, studying the computers in a desperate attempt to find out what was going on. “It must have full control of sublight navigation!”

“I thought all systems were clean,” Sumner’s voice said- McKay had almost forgotten that the Atlantis military commander was here, he’d been so quiet-, looking pointedly at McKay.

“They were,” he replied, shaking his head in frustration at the information before him. “When we did the reboot there was no sign of the virus; this shouldn't be happening!”

Whatever you’re doing down there, make it quick,” Caldwell said, his expression as frustratingly grim as ever (Would it be asking too much for them to get a military commander who tried to lighten the mood?). “Our current course is taking us towards a sun.”

McKay’s eyes widened in horror.

“A sun?” he repeated, looking incredulously at another console that displayed their current course. “Oh, this is bad…”

“At the risk of repeating myself, maybe we should focus on figuring out how this virus is still here after we allegedly wiped it?” Sumner asked, staring in frustration at McKay. “Preferably before we crash into the sun you’re so worried?”

“That is incorrect,” Hermiod said, looking up at Sumner as he studied his own consoles. “A more precise calculation of our heading shows that we will not collide with the star, but rather make a close approach, near its coronasphere. The ship will survive, but the radiation will kill everyone on board.”

Sumner could only stare in frustration at the Asgard, but stopped himself actually saying anything; right now he’d probably end up shouting at Hermiod, and the last thing he wanted was to get an Asgard angry at him, even if they didn’t seem the type to hold a grudge…

“Why kill everyone if they already have navigational control?” Elizabeth asked, voicing Sumner’s main question.

“The virus has access to our database,” McKay explained. “It knows our tactics, our tendencies-”

“Including the fact that we’d destroy the ship before we let them have access to it,” Sumner concluded, groaning as he stared upwards in exasperation, quickly realising what the Wraith had planned. “It’s one problem after another…”

And this time we don’t even have our secret weapon… McKay reflected, not even bothering to chid himself for the lack of logic in having so much faith in a man he still knew nothing about; after saving the city at least four times since they’d arrived there, he thought the Phantom had earned a degree of respect, to say nothing of a great deal of credit for his ability to handle so much crap that not even SG-1 had had to deal with…

“Wait a minute…” he said, snapping his fingers as inspiration suddenly struck him, looking eagerly around at the others. “There was a situation similar to this back at Stargate Command; I remember reading the report. An alien entity took control of the base computer, so they did a systems shutdown to destroy it; it survived by uploading itself into a MALP.”

“We don’t have MALPs-” Sumner pointed out.

“No, we've got a bay full of F-302s,” McKay finished. “We already know the virus can upload itself into the ship's navigational computer, but it could have used any one of those ships as a hiding place while we wiped the Daedalus systems clear’ it's the only possible explanation.”

“So…” Elizabeth asked, looking questioningly at McKay.

So,” McKay continued, with a slight smile on his face at the thought, “we physically pull the memory storage modules from the 302s, and then do another shutdown, and that should do the trick.”

“Right,” Sumner said, nodding in resolution at McKay before he glanced over at Elizabeth. “Contact the bridge and fill Caldwell in on the latest development; McKay, you’re with me.”

As he hurried through the Daedalus corridors towards the F-302 bay, Sumner made a mental note to recommend complete computer analysis be carried out on Earth ships every time they encountered the Wraith; the last thing they wanted was a repeat of this particular mess…

Still, in some ways, he couldn’t help but feel a certain satisfaction in the current situation. It might be difficult having to figure out a means of stopping a foe that could use your own ship against you, but at least he could be sure that he was solving this crisis on his own; he didn’t want anyone to start speculating that he was becoming complacent due to the present of the Phantom to help him out…

Then the door in front of him and McKay suddenly closed before they could go through it, and he knew that the situation wasn’t going to be that simple no matter how much he’d hoped otherwise.

“It’s not working,” McKay said, after his attempts to activate the door from the keypad failed.

“Let’s try another way,” Sumner said, refusing to consider the worst-case scenario as he led the way down another nearby corridor, only to be cut off by another closing door.

“It’s the virus,” McKay said, looking nervously over at Sumner after another attempt to activate the door failed. “It must know what we’re trying to do.”

“Great; a virus that knows what we can do to treat it…” Sumner groaned, shaking his head before he reached up to activate his radio. “Bridge, this is Sumner; are there any open paths to the 302 bay?”

That’s a negative, Colonel,” Caldwell’s voice replied after a momentary pause. “Looks like the entire section's been sealed off; we've tried to override it but we're not having any luck.”

“Right,” Sumner said, nodding grimly as he came to the only conclusion left available to them. “You’ll have to beam us in-”

“Wait; what?” McKay said, turning to look incredulously at Sumner. “The Asgard beam wasn't designed to beam from one point to another point inside a ship; we could end up rematerialised half inside a wall!”

“Right now, we don’t have much of a choice,” Sumner said grimly, trying to make it sound like he’d already known that; he had to at least give the impression that he was still in control if they were going to get through this. “We’ll have to take that chance.”

Right,” McKay muttered in exasperation, looking up at the ceiling as Sumner moved into position beside him.

“Ready,” Sumner said briefly into the radio; McKay looked like he was trying to scrunch himself up for some reason beside him, but the last thing Sumner had time for now was giving a near-hypochondriac a chance to relax even without the time limit they were facing.

Stand by,” Caldwell replied, McKay crouching down slightly as the colonel spoke. “Hermiod says we need to make a few adjustments first.”

After another few moments of waiting- during which McKay continued to do what even Sumner would have to describe as an attempted impression of a dwarf-, Caldwell finally spoke again to inform them that the transporters were active, moments before white light engulfed Sumner’s vision…

The light faded away almost as soon as it had appeared, revealing the fighter bay around them, along with the full compliment of F-302s.

“It worked!” McKay said, already straightening up as he spoke (Sumner decided not to think too much about the fact that McKay was surprised at that; the man might be smart, but it did him good to recognise that he wasn’t right all the time).

The Canadian scientist’s joy was cut off as alarms and lights began to blare all around them, followed closely by the bay doors at the other end of the room beginning to open…

Sumner didn’t need to have any kind of science degree to know that he was not going to like what would happen next…

Then he realised that the expected sudden ‘fall’ towards the doors and he and McKay were sucked out of the hanger along with the air wasn’t happening; actually, apart from the doors being open, the hanger seemed perfectly normal.

“We should really, really be dead right now,” McKay said, confirming that at least Sumner’s thoughts about the strangeness of this situation were accurate.

Colonel Sumner, Doctor McKay, can you hear me?” Hermiod asked, breaking the stunned silence that had settled over the two men.

“Affirmative,” Sumner responded.

I have raised the fighter bay shield in order to prevent the atmosphere from escaping,” the Asgard explained. “However, the virus has invaded the system and it is only a matter of time before it gains control; therefore, I suggest you complete your task as quickly as possible.”

Sumner didn’t need further information; moving as quickly as possible- grateful that he’d attended the briefings on the F-302s while back in the SGC; he might not have been planning on flying them but that didn’t mean he hadn’t been determined to make sure he knew everything about them that he could-, he hurried towards the nearest F-302 and pulled out its memory storage module, barely registering McKay doing the same as he hurried from one F-302 to the other, leaving the modules in the control chairs as he moved on to the next one; they should be secure enough there and carrying them around would accomplish nothing…

It was just as he reached the last F-302- McKay hurrying over to join him after removing the module from another; Sumner had a theory the scientist just didn’t like being alone for too long with the ship in its current condition- that Sumner heard a whistling sound that definitely wasn’t something he wanted to hear in this situation.

He barely had time to think before he acted; already crouched down in the F-302’s cockpit, he waved McKay into the rear seat before he closed the canopy over them, cutting them off from the rapidly-depleting oxygen supply outside the ship as the F-302’s own natural air supply activated.

“…Sumner, do you read?” Caldwell’s voice said; judging by the tone in his voice, he must have been talking over the radio for a while but Sumner hadn’t heard it.

“This is Sumner,” he said, taking a couple of deep breaths to regain the oxygen he’d lost before the canopy had closed. “Doctor McKay and I are fine; we managed to get into the last F-302 before we lost atmosphere, and all memory units have been pulled.”

Understood,” Caldwell said briefly. “We’ll attempt another emergency shutdown now; we’ll let you know when it’s done.”

With that, the radio communication was terminated, leaving Sumner sitting silently in the F-302 cockpit as he stared patiently at the sight before him. Fortunately the memory modules he’d removed earlier must have been positioned in a low enough location in the cockpits to be caught under the control consoles when he’d removed them, otherwise they’d have been sucked out with the loss of atmosphere, and everything else in the hanger was already bolted or strapped down in the event of such a problem…

“You know…” McKay said, drawing attention to the sound of rapid breathing taking place behind him, “I've never actually been inside one of these before today. It's a little… uh… cramped, huh?”

“Just relax, Doctor,” Sumner replied; he didn’t have time to pander to the astrophysicist’s claustrophobia. “We’re safe.”

“Great,” McKay said, even as the panicked tone in his voice made it clear that the situation was anything but great. “Quick question, though, just out of curiosity: how much, uh, air do these things carry?”

“Enough,” Sumner replied, his tone a brisk one that allowed no room for argument. “And it’ll last longer if you stay silent.”

He really wasn’t in the mood for another conversation with McKay as the scientist panicked about what might go wrong; right now, confined as they were, there was literally nothing they could do but wait until the virus had been purged from the systems.

A couple of minutes after that last exchange between them, the F-302 bay darkened as the power was shut down, followed by the lights coming back on a few moments later.

The system is clear,” Hermiod’s voice said over the radio, prompting a relieved sigh from Sumner as the hanger doors closed once again. “The virus is gone.”

Oh, thank God…” McKay said, slumping back in the chair in relief as Sumner clambered out of the F-302. “At least that’s over with…”

“Quite,” Sumner said simply, shrugging slightly as he looked at the astrophysicist. “So… are you going to sleep in there until we get back to Atlantis, or would you prefer to go back to your cabin?”

Chapter End Notes: 3: Well, it’s back to Atlantis in the next chapter, as Elizabeth discovers a very interesting clue in her search for information about the Phantom

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