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: 667602 Published: September 15, 2009 Updated: August 09, 2014
We're All Mad in Our Own Way by Marcus S Lazarus
Author's Notes:
This chapter will look at some of the events that occurred during the two-part "Lost Boys" and "The Hive", but obviously reference to the precise details of those episodes will be limited due to the majority of the action taking place off-world where John, naturally, cannot go; it's not the most extensive rewrite, but I think it allows for some good insight into John's character at this point in his history
As she stared out at the ocean before her, waiting impatiently for any sign of Atlantis's mysterious guardian to respond to her usual 'signal', Elizabeth wondered how wrong it was to be more concerned about the fact that she couldn't make contact with John than it was to be concerned about the now almost week-long absence of her military commander.

The more time she spent in this job, the more she began to appreciate how difficult it must have been for General Hammond back in the early days of the SGC; she might have lacked the general's practical experience at military matters, but she had at least entered Atlantis with relatively good- if primarily second-hand- knowledge of what kind of discoveries she might make out here in Pegasus, whereas Hammond would have been sending teams out into the galaxy with absolutely no idea about what he might be dealing with save for the knowledge of the Goa'uld's existence and their very real threat to life.

She just couldn't believe that things could have gone this wrong this quickly; the mission had seemed to be a perfectly straightforward assignment when it had originally come up. All they'd been doing was checking out a tip from one of Teyla's contacts about the location of a possible ZPM, and now Sumner and his entire team had been missing for several days with no sign of any kind of ransom demand or even a single unscheduled offworld activation that hadn't been immediately accounted for by a report from another offworld team, leaving them with no clue where the main team had gone and no idea what to do to find them.

Lorne and Zelenka were doing their best to run through some of the recently-dialled addresses from that planet's DHD, but given that they had no idea what order the addresses had been dialled in, it was still going to take ages to actually find what they were looking for, particularly since they had no guarantee that whoever had abducted Sumner's team would have stayed on the planet they went to after the original abduction; for all they knew the captors could have taken them to another planet afterwards...

"We have got to stop doing this," John said, his tone only slightly jocular as Elizabeth turned around to see him standing behind her in his usual relaxed manner. "Somebody's going to get suspicious at this rate; maybe I should set up a private phone-line..."

"Unlikely," Elizabeth replied, turning back to look at him with a brief smile. "Coming out here for air during a stressful situation is hardly that suspicious, and nobody ever comes out to bother me here anyway; it's a lot more straightforward than a giant floodlight in the sky, anyway."

"Quite," John said, smiling in a manner that gave no indication of whether he recognised the reference- he could have been smiling at the Bat-Signal reference or he could have just found the idea of attracting his attention in that manner unusual-, before he looked at her more seriously. "I can't do anything now."

"Oh," Elizabeth said, the smile fading from her face as she looked at him. "You're sure?"

"Positive," John replied with a solemn nod. "I'd like to help, believe me, but I've found nothing in the Ancient database that would allow you to carry out the current search at a quicker rate than what you're doing right now, and even if giving me access to the Stargate was possible, I can't contribute anything more than an extra pair of eyes to the current search effort."

"Good point," Elizabeth said, nodding briefly at him with a slightly sullen expression on her face, unable to stop herself expressing her slight dejection at the failure of this latest effort.

Then again, she supposed she should have expected this response from the beginning; she'd come here more out of habit than anything else. As John had made increasingly clear over these last few months since she'd returned from Earth, he could make mistakes and fail just as easily as any of them; there were times when even his evident skills couldn't make a difference to what they were dealing with...

"Well," she said at last, shrugging slightly as she indicated the door, the slight disappointment she felt pushed to the back of her mind once again, "I guess I'd better get back to work."

"Yep," John replied, smiling slightly back at her as he glanced upwards. "And I'd better get back to hiding."

Before Elizabeth could ask anything else, John had thrown what looked like a grappling cable from his belt towards a point above the balcony that she couldn't quite make out- she'd never been able to establish what all the various spires above them were for; they knew that some were transmitters and some were lightning-rods, but precisely which spires did what was still a mystery-, before pulling on the rope and sending himself flying upwards as though the line was on a reel of some kind, leaving Elizabeth staring up after him with a slightly stunned smile that swiftly faded into amusement.

"That's new," she said simply, forcing the smile from her face as she walked back into the control room; as amusing as it was to witness further evidence of the previously-perceived 'similarities' between John and Batman in the use of the grappling line he'd just demonstrated, if she walked in grinning when Sumner's team were still missing she'd attract far more attention than she wanted to.

After another couple of days with no progress, Elizabeth was increasingly finding herself contemplating drafting a letter to request official replacements for Colonel Sumner and Doctor McKay; Generals O'Neill and Landry might understand her reasons for continuing the search for Sumner and his missing team so far, but the IOA would only tolerate operations being suspended for so long before the expedition as a whole was ordered to resume their usual efforts to search for technology that they could use against the Wraith or the Ori...

The sound of the Stargate being dialled prompted her to get up from her seat and head for the control room, the shield dropping into place just as the seventh chevron of the incoming wormhole engaged.

"It's Doctor McKay's IDC," the technician at the Atlantis DHD said, looking back at her with a relieved smile that Elizabeth automatically returned.

"Lower the shield!" she said with a relieved grin, only half-noting the marines that were even now gathering around the Stargate; even if the new arrival turned out to be another Genii-esque attempt to take control of the city, at least they might have some information about what had happened to the missing team. For a moment, the sight of Doctor Rodney McKay walking through the Stargate brought a profound sense of relief to Elizabeth, and then she took in his appearance- wide eyes, constantly moving hands, a slightly silly grin on his face and perspiration lighting covering his skin as though he'd recently undergone some extreme effort of some sort-, and realised that the situation was still far from resolved.

"I know what I have to do!" McKay yelled as he walked through the gateroom, seemingly unaware or unconcerned about the guns around him (Elizabeth was better it was the first one; McKay would never be unconcerned about guns pointing at him).

"Rodney, what's happened?" she asked, looking urgently at the Canadian scientist, grabbing his arm before he could walk past her. "Where are the rest of them?"

"There's no time, no time," McKay said, his voice a rapid pace that Elizabeth had only heard him use in the past when he was feeling particularly frustrated or on-edge about something, pacing randomly around her as he waved his hands and breathed so rapidly that he was practically hyperventilating, his red-rimmed eyes doing little to console her. "The planet– not Ford's, the one the, uh, ship's headed towards-, we need to get there and we don't have much time; I was barely able to escape myself, but I managed to take out the guards."

He paused briefly at this point, but it was only to point at Elizabeth with a broad grin before he continued. "Oh, you should have seen me! I was amazing! I wish we'd got it on camera because... that's not the point!"

"Rodney," Elizabeth said, trying to control her immediate response- she had enough trouble right now without yelling at a man who was already clearly in a very difficult emotional state; she'd almost assume that he was high if it weren't for his overly-paranoid health concerns making it unlikely that he'd do this to himself-, "slow down. Are you all right?"

"Yes, yes," McKay replied, before he shrugged and let out a brief giggle (Elizabeth hadn't even known that McKay could giggle) before he began to pace again. "I mean, um... I dunno; I mean, I did take out the guards and they were huge and dumb and stupid and..."

"What guards?" Elizabeth asked, trying to sound more patient than she felt; McKay was hard enough to communicate with normally, but it was practically impossible with him in this condition...

"Ford's guards!" McKay replied, the brief moment of assertive insistence the closest thing to lucidity she'd seen him display since getting back. "Haven't I mentioned Ford?"

"No, you didn't," Elizabeth said, privately crossing her mental fingers at the reference to Ford; she was starting to get some ideas about what had happened to the rest of the team that she strongly hoped were the wrong ones. "And you haven't mentioned Sumner, Teyla and Ronon either."

"Yes!" McKay yelled, pointing triumphantly at her as though she'd just provided him with the missing piece of the puzzle that he'd been trying to solve. "They were there too, and there were the two guards; they were huge and massive and I had to take them out, so I had to inject some of the enzyme!"

"You took some of the enzyme?" Elizabeth repeated; she couldn't believe that someone as allegedly brilliant as McKay could have done something that stupid...

"No-no-no-no-no-no-no," McKay said, shaking his head as he continued to pace around her, his voice becoming increasingly high-pitched as he spoke, "I didn't take some of the enzyme. I took a lot of the enzyme, because I had to, because I had to take out the guards, which I did, and you should have seen me; I was amazing!"

"Are you insane?" Elizabeth hissed at him in frustration.

"Yes, yes," McKay replied, his face contorted slightly in pain as he spoke, evidently fighting to think his way through what he was saying. "Now that I've taken the enzyme, yes."

"Rodney, focus," Elizabeth said, grateful that at least the Canadian scientist had admitted to his current mental state; in her experience, if you were able to admit to being insane, you weren't so far gone that you couldn't be helped. "Where are the rest of your team?"

"No, no, no, I had to take the enzyme because... because I had to take out the guards!" McKay continued, talking as though he hadn't heard her before he began to pace again. "But that's not the point – the point is we don't have enough time; we need to stop the ship from getting to where the ship is going."

"OK..." Elizabeth said, placing an arm around McKay's shoulders in an attempt to guide him in the right direction. "Come on, let's take a walk to the infirmary, all right?"

"Whoa-whoa-whoa-whoa-whoa," McKay said, pulling free of her before they'd managed more than three steps. "What are you doing, where are we going? I don't wanna go to the infirmary, I wanna go to the, to the, uh..."

No sooner had McKay pointed at one of the side passages leading off from the gateroom than he collapsed to the floor, leaving the guards to hurry towards the scientist's fallen body.

"Doctor Beckett," Elizabeth said as she activated her radio, praying that what they were doing would suffice to help him, "we have an emergency; we're headed to you."

Sitting silently in the maintenance tunnel nearest to the infirmary, John could only listen to the low, weak and delirious rantings of the man that even the Elizabeth he'd originally met had called one of the most brilliant men alive- while making sure that he promised never to reveal that information to McKay if he ever found himself with the chance to tell his story to the expedition- and wonder at the sheer scale of what enzyme withdrawal could do to a person (Although he privately acknowledged that, based on what he'd heard Beckett say to Caldwell and Elizabeth earlier, this was probably the worst it would ever get, given that McKay was going cold turkey after taking a really large dose).

He'd known the stuff was dangerous, of course- the damage he'd caused to the rooms he'd locked himself in when he was 'detoxing' himself after particularly hard fights was proof enough of that; the door controls for a couple of the more distant rooms would probably never work properly after what he'd done to the control crystals before he'd stopped himself-, but his past experience with the stuff had been in relatively small doses on particularly desperate occasions, and even on his worst days he'd managed to burn through most of the enzyme fighting his way through the Wraith he'd been fighting at the time.

The sheer scale of what this stuff had done in larger amounts...

A part of him briefly wondered if it would have made any difference if he'd accepted Elizabeth's request/suggestion to help in the search- maybe he'd have been able to find McKay before the scientist had felt the need to do this to himself-, but he pushed that thought aside almost at once; he might be great at using Ancient technology, but he'd be the first to admit that sometimes the fine details of how some stuff worked wasn't his strong point, and hence there was nothing he could usefully contribute to the situation at this point.

And as for the possibility that the supply of Wraith enzyme he kept on him in case of emergencies could help McKay through his current state...

Given the minimal amount he possessed- enough for one, maybe two doses of slightly enhanced strength in a fight where he just needed an 'adrenaline rush' to push himself that but further; he always assumed when collecting the feeding sacks of the Wraith he'd killed that he just needed enough for the next fight and he'd 're-supply' then-, it wouldn't be enough; from what he'd seen and understood of Doctor Beckett's analysis, McKay had taken so much enzyme it had been practically a miracle he hadn't collapsed right away. The enzyme supplies he could offer were so minimal that they'd barely have given McKay any real relief, and would have essentially just made him take longer to come down rather than actually help him.

Plus, of course, the small, selfish part of himself that he hated to acknowledge the existence of reminded him, you wouldn't want to damage your 'noble warrior/vigilante' image with the good doctor, would you...?

As ashamed as John was to admit it, that part of him made a good point.

He might like to tell himself that he had also kept the existence of his enzyme 'stash' secret to stop Sumner becoming more 'jumpy' about him- the man might be scaling back the search for him since the Siege, but John wasn't going to kid himself that Sumner was any happier about having a renegade element active in Atlantis than he'd been when he first learned the Phantom existed-, but the thought of Elizabeth's reaction to him was another problem; the thought of her looking at him like she'd looked at Ford... wondering if he'd use it and attack her while under the influence... doubting him because he resorted to drugs...

It scared him.

More than that; it sickened him almost as much as the thought of her learning about the people he'd killed during the Genii invasion had done (Although he had to admit that she'd never really confronted him about it, he always felt anxious when talking with her in case she chose to bring it up).

He might not be worthy of Elizabeth's love, but he'd earned her friendship; he couldn't bring himself to do anything that could jeopardise that...

At least, not unless he was sure that there was no other way to accomplish anything.

He dreaded the thought of what would happen when that day came...

"How is he?" the object of his thoughts said, prompting John to glance out of his tunnel and see Elizabeth talking gently to Doctor Beckett, McKay now sleeping peacefully in his bed; he'd been so caught up in his own thoughts that he'd missed the moment when McKay's already-weakened delirium had finally led him to sleep.

"Asleep, finally," Doctor Beckett commented. "Mercifully..."

"Has he mentioned anything about Sumner and the others?" Elizabeth asked, a brief smile on her face at the reminder of McKay's usual attitude before she looked thoughtfully at the scientist, her gaze the same kind compassion her older self had directed at him when he'd first arrived in this city...

"No, not yet," Beckett replied, a slightly wistful smile on his face at the memory. "Our conversation was of a different sort; I feel not unlike the priest in The Exorcist."

For a moment John wondered at the specific details behind that reference- he'd never actually managed to see that movie, even if he'd found what he'd heard about it intriguing-, but then Doctor Beckett turned the conversation back to McKay's condition. "Well, he's through the worst of it. The nausea has passed, his pulse has returned to normal, blood pressure in a more reasonable range, considering he was borderline hypertensia before taking the enzyme."

"Good," Elizabeth said briefly.

"I hate to say it," Beckett added with a rueful smile," but his stubbornness is probably what sustained him through the ordeal."

"Hmm..." Elizabeth said, raising her eyebrows before she looked back at the doctor. "We won't tell him that, though."

"Aye," Beckett replied with a slight smile. "Mustn't feed the beast."

"No," Elizabeth agreed with a smile before her eyes returned to the Scottish doctor with that same universal compassion that was one of the things that he had loved about her since the day he met her. "You should get some rest; you look exhausted.

"I'll stay with him just a wee bit longer," Beckett replied, his attention turning back to McKay. "Just to make sure he's out of the woods."

Even as Elizabeth turned to leave, John had already turned around to head for his usual resting-area in this part of Atlantis; with McKay clearly out of the woods and nothing to be done until he woke up to explain what had happened to the rest of the team, he might as well get some sleep...

The next morning, Elizabeth was, for once, primarily relieved to see Doctor McKay enter her office without a pre-existing meeting scheduled; most of the times he came by unannounced had resulted in her learning about some bad news that she could certainly have done without- if she hadn't listened to his overly paranoid concerns about Chaya they might have been able to learn more about her before she sealed her Stargate address off from them-, but right now anything he had to tell her about what had happened would definitely be appreciated.

"Good to see you back on your feet, Rodney," she said, smiling briefly at the scientist as she stood up and walked around her desk. "You gave us quite a scare there."

"Yes, it was very strange," McKay said, shrugging slightly as he contemplated his earlier behaviour. "The whole time I was under the influence of the enzyme, it felt like I was, uh, I was perfectly lucid– eloquent, even; that it was you who wasn't making any sense or listening to reason. It was very peculiar. I think I kind of understand how Ford must have been feeling this whole time."

"Talking of Ford..." Elizabeth said, deciding that she might as well get straight to the current issue- if John had taught her anything in his time here it was the value of direct action in a crisis; diplomacy could wait for when there was more time to talk-, "what actually happened out there? And where are the others?"

"I don't know exactly, but I can probably figure it out," McKay said, heading for the main control room as Elizabeth followed him. "I told you Ford's alive?"

"It... came up," Elizabeth replied; it had been an unexpected bit of news, of course, but once again John had taught her not to take anything for granted no matter what you thought you knew. "What does he have to do with this?"

"He's been busy since we last saw him," McKay explained as he sat down at his station in the control room. "He gathered himself together a little gang, doped them all up on the enzyme. They're the ones that caught us, drugged us, and coerced Sumner, Teyla and Ronon to join them on a mission to destroy a hive ship."

"A hive ship?" Elizabeth repeated incredulously, leaning over to more directly address McKay.

"Yeah, they managed to steal themselves a Dart; like I said, he's been busy," McKay explained with a brief shrug. "Look, when they didn't return from the mission, I realised something had obviously gone wrong. Now, I have the coordinates to the planet that the hive ship was headed towards to cull."

"So, if the team's still alive- maybe captured on the ship-, there's a chance we can rescue them," Elizabeth concluded, hoping that her assessment of the situation was accurate; after the way things had been progressing on the search, any kind of information was a step in the right direction....

Later that day, the now-returned Sumner, Teyla and Ronon all resting in their quarters after their medical examination had concluded, Elizabeth was turning over Sumner's briefing in her mind, contemplating the new information that they'd discovered on this mission.

From what she'd gathered, Ford's plan to infiltrate the Hive by having Sumner pilot the Dart into it after 'culling' the rest of the team actually hadn't been that bad in principle- it might have been better with a more experienced pilot, but Sumner had taken a few basic flying lessons in the gateships recently and at least knew the essentials of what to do-, but the lack of resources on the part of Ford's team, combined with their limited knowledge about the fine details of the Dart's operating systems to begin with, had left Elizabeth feeling immediately sceptical about its chances. Even before she heard about how the Dart went into automatic pilot upon approaching the ship and two of Ford's team were lost before they were captured, it had been clear that Ford's use of the enzyme had reached a point where it was significantly impairing his judgement, and his later attitude on the hive-ship had only further reinforced that as he and Sumner apparently spent more time arguing with each other than they spent working on getting out of their cells.

In the end, they'd only managed to escape after the arrival of a second hive-ship at the planet where the culling was going to take place; after Teyla sensed their arrival, Sumner, using information Ford's men had gathered about division among the Wraith fleet- apparently the Wraith waking up so early meant that there was a 'food shortage' as the multitude of active Wraith found themselves at odds regarding how much they could cull now while still being sure of having a food source later-, had tricked the Queen of the Wraith hive by claiming that they were agents sent by the other hive to try and destroy the one they were on. When the Queen attempted to interrogate the rest of the team about Sumner's story, the still-crazed Ford, accompanied by the last of his team, had apparently attacked the Wraith soldiers, giving Sumner, Teyla and Ronon time to escape and find their weapons before departing the hive-ship in a dart, followed by Sumner using a trick that had been mentioned in an old SGC mission report- something about Apophis's first attempt to attack Earth directly, as Elizabeth recalled-, provoking the two hive-ships into attacking each other by firing on them in his dart before escaping to the nearest Stargate to return to Atlantis.

It wasn't the most organised mission ever, of course- three of her senior staff (Teyla and Ronon might not have any official ranks but she still regarded them as important parts of the command structure even if Sumner might argue the issue) had been temporarily technically addicted to drugs and Ford had almost certainly died when the Hive-ship exploded given that he was last seen fighting Wraith despite being heavily outnumbered-, but it had definitely turned up some useful information regarding the current social structure of the Wraith hives that they might be able to use at a later date...


That was the real problem here, really.

Ford might not have been a member of the expedition for the last few months, but he'd still been someone she'd brought to Pegasus; the fact that he'd died because of a position that she'd contributed to him being in...

There might have been nothing that she could have done to save the young lieutenant from himself- finding one man in an entire galaxy was far from an easy task, after all-, but that didn't realistically make her feel any better about his loss, particularly when she still had to write the official letter back to his family on Earth...

As he sat silently in the small 'junction' that served as his sleeping area- a location where a few of the maintenance tunnels he used to travel around Atlantis intersected to create a larger space-, John Sheppard raised a glass of the closest thing to a bottle of alcohol he'd ever managed to acquire during his time in Pegasus; he hadn't exactly had much chance to drink before he'd come to Atlantis, but he kept a couple around to 'treat' himself on special occasions.

"To Lieutenant Aiden Ford," he said, wistfully tipping his glass in memory of the now-deceased lieutenant (Blowing up a ship when the guy was still on it definitely didn't sound like something he'd survive, after all). "May he rest in peace."

He might not have particularly liked Ford- the man had been far too 'by-the-book' for his liking; at that age he'd hoped that the younger man would have displayed more 'on-the-spot' initiative rather than just relying on Sumner's plans to get him through the situation-, but his heart had been in the right place at least.

Besides... the day he was happy about the death of a human...

He didn't want to know what he'd be like on that day, but he strongly hoped that it never came to pass.

He might kill humans when he had to- memories of the Genii invasion flashed through his mind-, but he would never kill anyone simply because he wanted to do so...

If he didn't maintain a line like that, how long would it be before he became the monster he was always afraid that Elizabeth would witness inside him....?

He couldn't help but shudder at the thought of that happening.

Never, he silently vowed to himself.

He'd seen what he could become if he didn't care during the Genii invasion, and his brutality had horrified him in the aftermath; he could never allow himself to become that monster again...

He just wished he could shake the feeling that there'd come a day when he would be unable to keep that promise...

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