Mystery of the Phantom by Marcus S Lazarus
Summary: (AU, Part 2 of series) As their second year in Atlantis begins, Elizabeth finds herself drawn ever further into the mystery of the Phantom of Atlantis, while John finds himself constantly torn between what he has become and what he wishes to be...
Categories: Fanfiction Characters: None
Genres: Action & Adventure, Alternate Universe, Drama, Mystery & Suspense, Romance
Warnings: None
Challenges: None
Series: The Phantom of Atlantis
Chapters: 50 Completed: Yes Word count: 164646 Read: 667829 Published: September 15, 2009 Updated: August 09, 2014
Can You Hear the Bomb Tick? by Marcus S Lazarus
Sitting silently in his usual observation point above the main control room, John couldn't help but allow himself a brief hope that their current almost month-long record of time elapsing without encountering some kind of danger to Atlantis was about to be broken. The only currently-scheduled offworld mission was Doctor Zelenka's trip to check on the EM field on MGM-767- a mission that was pretty much guaranteed to be the proverbial cakewalk given the Wraiths' inability to land here (Where had that expression come from anyway... and he really needed to stop letting his mind wander at moments like this) even if he wasn't that happy about it-, the recent scans of a couple of passing Wraith cruisers firing at each other suggested that the recent Wraith civil war Sumner's team had learned about from Ford's men was still going on to great effect, Teyla and Beckett were heading off to the mainland to check on an old Athosian woman- he vaguely thought he remembered who they were talking about, but he wouldn't like to swear to it; keeping track of names wasn't exactly easy-, and McKay was still feeling uncomfortable about Cadman ever since she'd spent that time stuck in his head a few months ago...

Quite frankly, the most interesting thing that seemed set to happen today was the current dial-up to Earth to update them on their latest progress, and even that was relatively uneventful; so far nothing overly interesting had been discovered in Atlantis that they hadn't known about already...

Then John heard McKay yelling at them to stop dialling before they had input the last two chevrons, and he instantly re-evaluated his earlier assessment; it sounded like things were just about to get a bit more interesting...

Even as she walked into her office after hearing the latest news, Elizabeth almost couldn't believe it.

The Trust had planted a bomb in Atlantis?

She'd known that the renegade NID organisation had become the most powerful Goa'uld based organisation in existence following the fall of the System Lords last year, but the idea that they'd acquired enough influence to get an agent all the way out here in Atlantis...

That terrified her almost more than the thought of how close they'd all come to being destroyed did; threats to her life were something that she'd almost grown used to, but the scale of the Goa'uld's reach was a definite point of concern...

"We need to disconnect the ZedPMs and switch to back-up naquadah generators to prevent any possible dialling of the gate to Earth," McKay said, the immediately-available senior staff of Atlantis now gathered in her office to discuss what action they should take next.

"I agree," Elizabeth confirmed with a brief nod. "In fact, as of this moment, all 'gate activity should be suspended; how many offworld teams do we have out there?"

"Zelenka's team on M7G-677 is pretty much it, and they can safely be left where they are for the moment; it's not like the Wraith can get there anyway, and the natives are friendly enough," Sumner said briefly; he'd never been a particular fan of the inhabitants of M7G-677 when he'd been there, unable to bring himself to comprehend their 'suicide pact' even after McKay learned of the alternate explanation for why the founders had imposed that 'rule' in the first place. "I assume the Daedalus is still in range to relay a data transmission back to the SGC?"

"Yes, they're, uh, holding a position that keeps them in range of both Earth and us," McKay responded.

"Good," Sumner said with a brief nod. "Let them know that we received their message and aborted the dialling, and see if they can tell us more than 'there's a bomb in Atlantis'."

"The Trust probably think this is the only way to make sure that the Wraith don't back to their galaxy," Elizabeth put in, drawing the focus of the discussion back to the more central issue of the bomb's origins rather than their current lack of information about it.

"Well, it's drastic, but effective," McKay admitted with a brief nod.

"What's worse," Elizabeth continued, looking around at the others to ensure they understood what she was about to tell them, "is that the Trust operative who planted the bomb probably did so under orders from the Goa'uld."

"What?" McKay yelled, looking in shock at Elizabeth.

"Yeah, I remember that file," Sumner said, nodding in understanding at Elizabeth before he looked over at McKay. "The Goa'uld infiltrated the upper leadership of the Trust several months ago, giving them a stronghold on Earth and access to various government agencies; with the System Lords having been virtually wiped out, it's probably the most powerful Goa'uld-based organisation left in existence."

"What's a Goa'uld?" Ronon asked (Elizabeth couldn't help but feel somewhat frustrated at herself after that last statement; Ronon had spent so much time working with them and yet they'd failed to tell him virtually anything about the enemies they'd faced back home).

"Essentially," Sumner said as he looked over at the Satedean, "a Goa'uld is an alien snake that can enter peoples' heads and take control of their bodies; they ruled a substantial portion of our galaxy in the past by posing as gods."

"They don't sound pleasant," Ronon said in what was probably a reflective manner for him.

"Trust me, they're not," Sumner said briefly, his grim tone a reflection of his prior contact with the Goa'uld during his time affiliated with the SGC prior to his arrival in Atlantis as he turned to Elizabeth. "I'll organise teams to examine the most likely sabotage locations where a bomb might be stored."

"I'll check primary and secondary systems for any anomalous energy readings that might indicate the presence of an explosive device," McKay added.

"And I'll do what I can to contribute," a voice said from the door, prompting the group to turn around to see the Phantom standing at the door, his arms folded under his cloak and the technicians in the control room all looking uncomfortably at the man in the mask as though uncertain whether they should have done something to stop the Phantom reaching the office.

"Phantom?" Sumner said, glaring slightly at the figure in the door. "What are you doing here?"

"As I said, I'm here to help; nobody knows the fine details of Atlantis's construction like I do," the Phantom replied (Elizabeth noted that he was taking care not to look at her, but made a mental note not to be upset at this decision; it wasn't like he could show too much attention to her without risking giving away their secret contact with each other). "Add in the fact that you can guarantee that I'm not an agent of the Trust, and I think that it's fair to say that you can't exactly ignore my help."

After a moment's brief silence as he stared at the Phantom, Sumner nodded.

"Point," he said simply. "I'll assume that, in exchange for your assistance, you want confirmation that we won't attempt anything... untoward?"

"Precisely," the Phantom nodded. "Add in the fact that I can assure you I'll provide you with something useful at the conclusion of this particular affair if you let me handle this my way, and..."

He shrugged. "Trust me; it's in your best interest to give me relatively free reign in tackling this situation."

"Agreed," Elizabeth confirmed, allowing herself a brief smile at her... friend, she supposed would have to be the best term... as he walked into the office. "Do you have any-?"

"You're the Phantom?" Ronon said, his gaze giving no indication how he felt about this meeting.

"I am," the Phantom replied, nodding briefly back at Ronon. "And you're... from Satedea, correct?"

Ronon didn't answer verbally. Instead, he stood up, walked over to stand in front of the Phantom, and launched a single punch at his face, the resulting clang of metal being struck making it clear that Ronon had hit the Phantom's mask with exceptional force even if the subsequent appearance as the Phantom regained his balance after the punch gave no indication that his mask had been damaged in any way.

"Let me guess... for not being there for Sateda?" the Phantom asked, his stance giving away just as little about his feelings on the matter as Ronon's own.

"Pretty much," Ronon replied. "Probably couldn't have done anything if you were there, I admit, but it's the principle of it."

"I understand," the Phantom responded with a brief, accepting nod. "Just so long as you believe me when I say that I would have done whatever I could to be there when the attack came if I'd known about it..."

"I get that," Ronon nodded. "Big galaxy; you can't be there all the time."

"Thanks," the Phantom said, before he turned to look at the others, both men clearly having said all that they wanted to say at this time. "OK; what have we got so far?"

"Well, Lieutenant Cadman's going to be assigned to the search- she's one of the best bomb experts we've got-, but that aside all we can do right now is track this bomb down and take it from there," Sumner said simply. "Once we know where the bomb's been planted, we can work out who planted it from that point onwards."

"Good strategy," the Phantom said, as he walked around Elizabeth's desk to indicate the computer. "If I may; I've got a better idea of where a bomb hasn't been planted at this point than you do."

"Go ahead," Elizabeth said, nodding briefly at him as he sat down and pulled up a map of Atlantis before she turned to the others. "We'd better ask Colonel Caldwell to return here to assist in the investigation."

"What?" Sumner said, looking at her. "We'll be cut off from Earth if Daedalus comes back here-"

"True, but it's also the best way to question whoever on board that ship may have been responsible for planting the bomb here in the first place," the Phantom said as his fingers continued to tap away at the keyboard with a casual familiarity that nobody present was sure what to make of.

"Precisely," Elizabeth confirmed, before she looked around at the others. "Alright, let's get moving; we have a bomb to shut down."

With both of the city's ZPMs now disconnected from Atlantis- the original ZPM might have been down to around a tenth of its original power at best but even that was enough to trigger a decently-sized explosion if it was triggered under these circumstances-, the search progressed relatively swiftly, particularly with the Phantom's 'inside information' able to eliminate certain parts of the city from the search effort such as the pier power distribution sensors (Sumner made a mental note to ask the Phantom how he knew about those areas once this was over, even if he doubted that the Phantom would give up that information as part of his 'agreement' with them; he was only just willing to believe that the Phantom was willing to help them keep the city intact after the effort he'd put into defending it until he received incontrovertible proof of the Phantom's true agenda). The latest news relayed from Earth via the Daedalus was able to confirm that the 'trigger' that would detonate the bomb had been planted on Atlantis rather than back on Earth, which at least gave them a slightly better idea of what to look for, but that didn't help matters when they still didn't know where to look.

"Nothing on the grounding stations," Sumner said over the radio as his team completed their survey.

"Understood," Elizabeth said, nodding into her radio at the latest report as she glanced over at where McKay and Cadman were going over the internal sensor readings with the Phantom (Cadman and McKay might be able to identify unusual energy signatures, but the Phantom would have a better idea if the signals were meant to be there in the first place). "Be advised; we just received a second message-"

"DHD!" the Phantom- she couldn't think of him as John; the possibility of a mistake was too great- suddenly yelled, dashing over to the dialling device just as it began to dial what even at Elizabeth's current distance looked like Earth's address, only for the Stargate to shut down before it could complete the program.

"Hah!" McKay said, grinning as he joined the Phantom in looking at the DHD before glancing back at Elizabeth. "Good thing I pulled the ZedPM; whoever planted the bomb must have devised a programme that would upload itself and automatically dial the gate if the first dialling was halted-"

"As well as transmitting a distress beacon?" the Phantom said, glancing over McKay's shoulder at the screen on the wall, showing a dot on one of Atlantis's piers emitting a signal of some sort.

"Oh, no...!" McKay groaned, staring at the screen in frustration. "The 'gate dialling itself was just a means of drawing our attention away from this-!"

"Not any more," the Phantom cut in, walking over to one of the Ancient consoles and tapping a couple of buttons, shutting the system down with what almost looked like a flourish as he turned back to the others. "Sorted."

"Not quite..." McKay muttered, walking over to study the long-range sensor screen with evident apprehension before looking back at the rest of the staff. "The damage is already done; those two Wraith cruisers we detected earlier have altered course and are heading straight for Atlantis.

"Damnit..." the Phantom muttered, looking upwards in frustration. "No wonder we're not finding anything..."

"Pardon?" McKay said, looking at the Phantom inquiringly. "What's that meant to mean?"

"Come on, look at the facts here; the person who planted the bomb diverts our attention so that the distress beacon can be activated at a moment when a couple of Wraith ships are going to be able to pick it up?" the Phantom said as he stared pointedly at McKay. "What does their approach mean we'll have to do?"

"Uh... cloak the city?" Chuck the technician put in, looking slightly uncertainly at the Phantom (The junior staff were still evidently uncomfortable with the Phantom's presence in the control room; even if he was helping them, the man made for an imposing figure).

"Bingo," the Phantom confirmed, nodding briefly at Chuck before turning back to McKay. "And what do activating the city's cloak and dialling an inter-galactic wormhole have in common?"

"They both need the ZedPM to work-" McKay began, looking at the Phantom with an expression that suggested he was having to explain to someone how to use two and two to make four.

"Exactly," the Phantom said with a nod. "Blowing up a couple of Wraith ships wouldn't make any real impact on the Wraith fleet as a whole- even with the numbers they lost in the recent siege there's still around fifty hive-ships out there, and these aren't even hives, they're just cruisers-, but what if our bomber wants to put us in a position where we have to use the ZPM?"

"Of course..." Cadman said, her eyes widening in understanding as she turned to McKay. "You've always emphasised the explosive power of the ZPMs; if one of them exploded-"

"And if someone shut down the failsafes that stop it from exploding in the first place by leaving us unable to control the amount of power we're drawing from it at any one time..." McKay continued, horror dominating his face as he thought about the implications. "Oh my God..."

"Precisely," the Phantom said grimly, nodding at McKay as he indicated the nearest laptop. "Well, best get down to business then, right?"

"What do- oh, reactive the failsafes," McKay said, nodding in understanding as he sat down at the screen and began to tap rapidly at the laptop, pulling up the relevant systems and cursing after a few minutes' analysis of the code. "Ah, crap..."

"What?" Elizabeth asked uncertainly.

"Evidently, whoever set this whole thing up isn't as idiotic as we are," McKay said, staring in frustration up at the Phantom. "Whoever was responsible for shutting down the failsafes not only set it up in such a manner that the city's sensors didn't detect it, but also added in a code to block access to the systems necessary to reactivate them."

"OK," Elizabeth said, nodding slightly at her head scientist. "With that in mind, our first priority should be to disable the DHD- it's the quickest means of drawing power from the ZPM-, and then get on with turning those failsafes back on."

"I'll get right onto that," McKay said, getting up from his seat and walking over to the DHD, before he paused and looked back at Elizabeth with an uncertain stare. "Unfortunately, any number of systems can be used in conjunction with each other to, uh, overload the ZedPM; it'd be a much more gradual build-up than dialling the Gate, which would cause an instantaneous power spike, but, um, equally as effective in its results."

"And we still need that ZPM to activate the cloak when the cruisers get here..." Elizabeth groaned, nodding in understanding of McKay's point.

"On the bright side, dealing with the Wraith once we've got the cloak up is simple enough," the Phantom added, smiling slightly over at Elizabeth, even as the grimness of his gaze made it clear that he recognised the continued problem of getting the cloak up in the first place. "If you take a transmitter and dump it- along with some charred rubble- on a beach on the mainland, they'll probably assume it's just jetsam that washed up when the city exploded during the siege."

The smile faded as he turned his attention back to the code in front of him. "The problem now is working out who among our suspects had the technological know-how to add something like this into systems I don't even understand..."

"Hold on; you don't understand these systems?" Chuck asked, looking at the Phantom in surprise before McKay could voice his own thoughts on that topic. "But you've lived here for decades-"

"I know enough to get by; that's not the same as knowing enough to change things," the Phantom explained. "I've got a good working knowledge of how Atlantis works, but don't ask me to change any of the fine details of its operating system; that's a bit beyond my abilities..."

Looking at the masked man who'd helped to save the city so many times, Elizabeth wondered what it was about that statement that made her feel uncomfortable; he was being remarkably casual with people he'd only just met-

Then it hit her.

The Phantom was lying.

He wasn't lying completely- he was definitely telling the truth about the fact that he didn't know much about how to change Atlantis's programming code; she hadn't become a diplomat by being easy to lie to-, but she doubted he was as ignorant of it as he claimed he was...

Still, it wasn't her concern; anything that helped John remain safe without compromising Atlantis was fine with her (And when had she reached the point where those two were almost of equal importance to her?)...

Shaking her head to push those thoughts aside, Elizabeth turned her attention back to the matter at hand; with McKay having confirmed John's theory about what the Trust spy had done to set Atlantis up to explode, that left them with only a relatively small suspect list to choose from, and right now- if her memory served her correctly-, the man who'd have to be her prime suspect for this whole mess was currently on board Daedalus...

So much for maintaining contact with Earth, she thought, as she turned around to look at the technician currently monitoring Atlantis's long-range communications systems to keep them in touch with Daedalus.

If her current theory about the person responsible for this latest threat to her city was correct, not only would they have to abandon any thought of regular contact with Earth to directly question their suspects, she was about to have to deal with some issues regarding the methods used to get the information they needed that she was not looking forward to confronting...

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