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Author's Chapter Notes: AN: Some medical details here regarding dislocated limbs that I'm not that sure about- along with a couple of general details about the chapter as a whole that I'm a bit ambiguous about-, but it was the best thing I could think of for the events depicted that wouldn't cause any serious long-term damage so long as the person responsible knew what they were doing

A couple of hours later, Daedalus now in orbit of Atlantis and the passenger manifest having been transferred down to them to check for any inconsistencies- the possibility that someone had sneaked on board Daedalus after planting the program in Atlantis's systems to escape being caught in the explosion at this end couldn't exactly be overlooked-, Elizabeth found herself sitting silently in her office as she studied the personnel files before her, wishing that she could avoid this duty.

She might be used to suspecting people of having ulterior motives when she was drawing up treaties in the past- making sure that everyone got something out of the treaty without appearing to favour one side over another was never easy-, but that was when dealing with people that she didn't know personally; when faced with the possibility of suspecting someone that she knew- and most likely someone that she had appointed to a position in the first place-, it was far more difficult to be objectively rational...

"Problem?" a voice asked.

Glancing up, Elizabeth couldn't stop a slight smile at the sight of John standing in the door of her office, looking at her with the slight concern that was all she could realistically expect from him in the current circumstances (Sumner accepting his aid during this crisis was one thing, but the knowledge that Elizabeth had made prior contact with the Phantom probably wouldn't go down very well). There might have been a guard standing just at the end of the corridor with his gun not-quite-aimed at the Phantom in the event that he tried anything, but somehow, Elizabeth couldn't shake the feeling that it felt... right... for John to be able to drop in on her like that, rather than their secret meetings on her balcony...

"Just the obvious," she replied, pushing those thoughts to the back of her mind as she looked back at him. "Having to suspect one of our own..."

For a moment John's mouth seemed to twitch in a slight smile as he looked at her- it was only when she realised that she'd just referred to the Atlantis personnel as 'our' own as though she and John were the heads of the Atlantis expedition rather than her and Sumner; the fact that John was slightly pleased about that inspired something that even she wasn't sure how she felt about it-, but then the smile faded as he looked at her.

"If it's any consolation," he said, his voice slightly lower as he walked towards her- evidently he didn't want the rest of Atlantis's staff to know just how much he knew about them; Elizabeth still wasn't entirely sure how to feel about the fact that he trusted her more than he trusted the rest of her staff-, "I do have one obvious candidate you might want to question first, and I have a few small ideas about how to get more out of him if he proves initially uncooperative..."

"You think I did it?" Doctor Kavanagh said, looking in evident frustration at Elizabeth; clearly his transfer back to Earth had done little to improve on his original attitude to life on Atlantis.

"Relax, doctor," Elizabeth said, walking around the small table they'd set up in one of the conference rooms to enable a more direct interrogation of their suspects. Getting Caldwell to agree to these interviews being conducted on Atlantis hadn't been easy, particularly when he'd insisted on questioning those on board his ship before she did, but Elizabeth and Sumner had convinced him to leave it alone by pointing out that the investigation fell under Atlantis jurisdiction and they were therefore the ones who would be responsible for the interview. "You're just one of many people I'm questioning-"

"No, I'm pretty sure that mine's the first on what is probably a very short list," Kavanagh countered, his eyes flicking briefly over to the marine standing guard at the room's door before turning back to glare at Elizabeth.

"Shortly after the siege, you couldn't wait to leave Atlantis," Elizabeth elaborated (She couldn't allow herself to think about what Kavanagh had just said; the fact that he was accurate about being only one of a few suspects didn't mean it was something she liked to consider in depth). "A few months later, I received an urgent request from you to be allowed to return. Your second tour lasted three weeks, and suddenly you asked to leave again-"

"Yeah, because working conditions were intolerable for me here," Kavanagh interjected. "I have no friends here, my work is not respected-"

"And this occurs only days before we discover that someone with excellent computer skills has managed to rewrite Atlantis's operating systems and disable the failsafes that prevent the ZPM from overloading," Elizabeth countered herself, leaning forward slightly as she continued to stare coldly at him. "Add in the fact that you were very eager to leave the city before it happened-"

"Oh, so obviously I did it!" Kavanagh spat in frustration, sitting back and folding his arms as he glared scathingly at her.

"Given the circumstances, I'm sure that you can see how that behaviour could arouse suspicion?" Elizabeth countered, trying to sound reasonable despite her growing frustration with the man before her.

"Your suspicion, sure," Kavanagh retaliated. "Seeing as how you never cared for me, nor valued the talents I brought to this expedition."

"My personal feelings towards you, no matter what they may be, have nothing to do with this," Elizabeth replied, even as she made a mental note to actually look up whether Kavanagh had actually contributed anything to their time here that she should know about; as much as she disliked him, it was possible that she might have ignored his better work because of her personal prejudice against him rather than because it hadn't been that good...

"Oh, please!" Kavanagh spat, dashing any thoughts of sympathising with him out of Elizabeth's mind. "Everything you do is motivated by personal feelings. You're driven by emotion, not reason! It's why I've always felt you're not capable of doing this job; you don't have the-"

Noting the glares he was starting to receive from Elizabeth and the marine at the door, Kavanagh stopped himself finishing with the word he'd been originally planning to use and amended his choice to, "...strength... to be leading the fight against the Wraith."

"If I remember correctly, you were the one who wanted to- what was it?- run and hide?" Elizabeth asked, her arms folded as she glared critically at the man before her.

"And at the time, I was right; if the Daedalus hadn't arrived at the eleventh hour, this city and everyone in it would have been wiped out because of your recklessness," Kavanagh countered with a scornful snort. "There's no need for The Trust to blow it up when Doctor Weir's at the helm!"

Elizabeth stopped herself from making her desired automatic response that the expedition had actually been doing rather well even before the Daedalus arrived thanks to the assistance of the Phantom...

And that was even before she factored in Kavanagh's own lack of contribution to the siege; from what she recalled of McKay's staff evaluations of his team's performance during the siege, Kavanagh had been rather uncomfortable with their reliance on the Phantom, spending most of the time working on his own separate computer while everyone else focused on a group effort involving working out the timing of the bombs or how to extend the punishment the shield could take...

"Seeing as how this isn't getting us anywhere," Elizabeth said, standing up and glaring pointedly at Kavanagh, "I'm going to let someone else take over here."

"Oh God; you're doing 'Good Cop, Bad Cop' now?" Kavanagh groaned as he stared after her as she walked to the door of the conference room. "You can't be serious-"

As Elizabeth closed the door behind her, cutting off all but the loudest sounds within the room from the outside world, she could only hope that her faith in John wasn't misplaced; if he actually went as far as he'd gone when fighting the Genii- that secret, shameful part of herself couldn't stop her from remembering the condition that some of the bodies had been in when they'd been discovered, faith in John momentarily outweighed by the memory of the brutality of what he'd done-, then the chances of Sumner or anyone at the SGC accepting him taking a larger role in the city were virtually nonexistent...

Further thoughts from Kavanagh were cut off as the door to the conference room closed, followed almost immediately by someone grabbing Kavanagh's arm and pulling it rapidly backwards with a clearly audible 'pop', Kavanagh only just opening his mouth to scream before a gloved hand was clapped over it almost automatically.

"Make a noise and this stays dislocated for the duration of our 'chat'; stay quiet and I put it back," a voice practically growled in Kavanagh's ear. "Clear?"

After Kavanagh managed to collect himself enough to nod, he was treated to another sharp burst of pain as his arm was reset- there'd be some sore ligaments, but from what he could tell it didn't feel like his arm was going to have any severe damage as a result of what had just happened to it- before the attacker casually sat down opposite him, revealing a masked face that Kavanagh instantly recognised.

"Phantom..." he whispered, his face growing pale almost automatically.

"Bingo," the Phantom replied, in that low, slightly guttural voice that had left Kavanagh so uncomfortable the last time he'd heard it. "Now then, let's cut to the chase; what is your connection to the Trust?"

"I don't have-" Kavanagh began.

"You have an extremely low opinion of Elizabeth's way of doing things, you favour methods that would endanger others over methods that might put you yourself at risk, you definitely have the technical knowledge to modify the Atlantis failsafes to set up our current predicament involving the ZPM being set to potentially overload if too much power is drawn from it at once, and when you factor in the fact that you were very eager to leave here when Daedalus departed- to say nothing of the fact that the team searching for clues noted that you sent three encrypted messages to Atlantis on your way here-, well..." the Phantom said, his eyes narrowing as he stared at Kavanagh.

"So... what?" Kavanagh countered, trying to assert himself; he wasn't going to admit to being afraid of a renegade masked vigilante (Even if he was afraid of the guy; his arm still smarted from the dislocation). "I wanted to make sure a few friends were all right; you're just assuming I'm guilty until proven innocent-?"

"I'm assuming as such until you give me clear, concise evidence that you're not responsible for our current situation, and so far your current attitude does little to make me think otherwise, particularly when you just said that you were trying to send messages to your friends here after saying earlier that you left because you didn't have any," the Phantom countered, standing up and leaning over the table to glare at the other man. "So, either start cooperating- I might be willing to assume you were exaggerating your social status earlier for dramatic effect-, or learn just how much damage and pain the human body can endure without any serious damage being caused to any part of you..."

"You wouldn't," Kavanagh said, staring coolly back at the Phantom. "You put too much value in Doctor Weir's opinion; did you think I wouldn't realise why you went to the bother of threatening me to edit my message back to Earth? You need her to-"

A sharp kick to the right kneecap left Kavanagh momentarily screaming in pain before the second kick knocked the kneecap back into place, the pain shifting to a lower-but-still-noticeable level as the Phantom glared at him.

"When it comes to the safety of Atlantis," the Phantom said, his eyes narrowing as he looked at Kavanagh, his fingers tapping slightly on the table before him as though he was itching for an excuse to attack the man before him, "I can assure you that little details like one woman's opinion of me matter very little... particularly when I am dealing with someone who has already provided me with ample evidence to lead me to the conclusion that he would welcome the Trust's method of doing things so long as he was absolutely certain that he himself would be at no risk."

"You psychotic-!" Kavanagh began, still clutching at his throbbing knee.

"Your insults mean little to me, and your threats even less," the Phantom said simply. "I will say this again, Doctor Kavanagh, and this time I expect a clear answer or we'll move on to seeing just how much damage I can do to your fingers without breaking anything; did you plant the code in Atlantis's computers?"

"NO!" Kavanagh screamed, as the Phantom reached under his cloak and pulled out his gun. "I didn't do it; I didn't do anything, I just want to get out of this psychotic facility that allows an overly emotional woman to use a deranged lunatic as-"

The sound of the Phantom's gun being fired was the last thing Kavanagh's senses registered before he was rendered unconscious.

"He didn't do it," John's voice said as Elizabeth stood in the control room with her senior staff, the team going over the various lines of code to try and determine the most effective means of reactivating the failsafes.

"Excuse me?" McKay asked, turning from the screen where he and Lieutenant Cadman were going through the various lines of code to look at the masked man uncertainly. "Who didn't do what?"

"Kavanagh might be a prat, but he didn't shut down the ZPM failsafes," John said by way of explanation, his tone brisk and his arms folded in a manner that made it clear that he wasn't that interested in discussing the current topic in greater depth than he had to. "I... gave him good reason not to lie to me, and then I stunned him; he should be out of the equation for now and we can focus on the more immediate matter of finding the code."

"And you're sure he's innocent?" Sumner put in, his eyes narrowing as he looked at the man he had formed an unwilling alliance with. "I'm sure I don't need to remind you that time is a crucial factor right now-"

"As I said, I gave Kavanagh a good reason not to lie to me," the Phantom replied (When John was this direct, Elizabeth couldn't entirely bring herself to think of him as 'John'; this was the Phantom that had made the Wraith afraid, not the man who'd risked everything to save Atlantis). "Trust me; he's not the man you're looking for right now."

"Well, given that he was pretty much our prime suspect because you suggested he was, that doesn't leave us with a lot of options right now!" McKay said, waving a frustrated arm at the Phantom even as he returned his attention to the computer screens before him. "I've been going over everything we've got and I'm still no further along in cracking the code to get those failsafes back up and running, and those Wraith cruisers are just getting closer..."

"Uh..." Lieutenant Cadman said, looking uncertainly back at the rest of the senior staff. "Actually, I did notice something that might be relevant earlier."

"Such as?" McKay asked with an impatient glance over at Cadman.

"Well, when I was going over the communication logs for Daedalus, apart from some encrypted messages from Kavanagh that we're still working on, I noticed some anomalies in the system command logs from the last few months," Cadman said, looking slightly uncomfortably at the stares she was receiving from Sumner and McKay. "There's a couple of gaps in the data streams from a few weeks ago; it's probably nothing..."

"If something's been deleted from the records at that time frame, it could have what we're looking for," Elizabeth admitted with a thoughtful nod.

"Do we really have to-?" McKay asked.

"We have enough time before those cruisers get here to explore that possibility; if this could turn up anything about who's responsible for this, we have to explore it," Elizabeth said, nodding resolutely at the young explosives expert. "See what you can turn up with that; in the meantime, Doctor McKay can continue searching for the code."

Standing in the conference room a couple of hours later as the Wraith cruisers continued to approach them- the Daedalus was still waiting near Atlantis in the event of an evacuation becoming necessary if they were forced to raise the cloak-, Kavanagh having been taken to the infirmary to recover, Elizabeth was surprised that she was more apprehensive about the current confrontation than she was about who she was in the room with, even after witnessing the evident issues both men had with each other.

Colonel Sumner and the Phantom might be looking at each other from either side of the conference room table as though they were each waiting for the other to give them an excuse to start fighting- Doctor Beckett's report that Kavanagh's arms showed signs of dislocation had done little to Sumner's opinion of the Phantom; Elizabeth was almost certain that John had lost much of his previously-gained credibility with that action-, but she was nevertheless confident in their ability to handle the current problem with a reasonable degree of control regardless of their issues with each other.

If anything, she was almost disturbed at herself at how willingly she'd accepted the news of what John had done to Kavanagh. She didn't condone torture herself, of course, but she could see how John might have felt that it was necessary to resort to those methods in the first place, and it wasn't like they hadn't had good reason to assume that Kavanagh had been up to something; so long as he hadn't caused Kavanagh any actual permanent- or even seriously long-term damage-, she couldn't bring herself to feel that concerned about what had taken place...

The transporter activating and depositing Colonel Caldwell in the room with them cut off any further self-analysis Elizabeth might have been planning to make regarding her feelings about what John had done to Kavanagh; right now, a saboteur had to be questioned.

"What the hell's going on here?" Caldwell said, looking in admittedly very convincing confusion at the people around him as he stood up to face her more directly (John had already moved back into the corner of the room, Elizabeth noted; evidently he wanted to be out of immediate range of any attack but also be ready to act if he had to).

"I asked Hermiod to beam you here so that you could give us the access code," Elizabeth replied.

"What?" Caldwell said incredulously.

"Lieutenant Cadman discovered a gap in the system command logs that indicated two deletion points that she had-" Elizabeth began.

"Look, we don't have time for this!" Caldwell protested, glaring between Atlantis's two commanders.

"Your identification code was used to identify this city's operating system," Elizabeth continued as she walked forward, ignoring the indignant expression on Caldwell's face. "You copied it and took it back to The Trust, whose Goa'uld scientists then rewrote the programme to overload the ZPM. You then brought it back here and uploaded it into the Atlantis computers."

"You think I'm working for the Trust?" Caldwell asked, a slightly stunned, incredulous smile spreading across his face that made it clear that he couldn't believe what he was hearing.

"We know you're working for the Trust," Sumner informed his Daedalus counterpart, drawing his sidearm from its holster and cocking it. "Give us the code and this doesn't have to get ugly-"

The sudden golden gleam of Caldwell's eyes instantly halted any thoughts Elizabeth might have had of simply reasoning with him.

Caldwell was a Goa'uld host...

"I will never give you that code," the creature using Caldwell's body said, using the same dual-toned voice that Elizabeth had heard far too many times during her failed 'negotiation' attempts during her few short months in charge of the SGC.

"I warn you," Caldwell's Goa'uld continued, even as Sumner raised his pistol to aim it at the other man's head, "as a Goa'uld I now possess the strength of many men."

"Nice threat," John said, prompting the Goa'uld to turn around and face him as he walked out of his corner, Elizabeth taking a few quick steps back to avoid any chance of being caught in the seemingly-inevitable crossfire. "Too bad this isn't the kind of fight where that kind of advantage counts for anything."

Before Caldwell- or at least the creature now inside him- could respond to that statement, John had kicked his opponent in the chest with such force that even the Goa'uld-enhanced host was knocked to the ground, promptly pulling a taser gun out of his cloak and firing the electrodes at the man's chest, leaving Caldwell tensed in pain as electricity pulsed through his body, his eyes briefly flashing as John briefly turned the voltage off only to turn it back on again.

"Hold on, you-!" Sumner began, only for John to shoot him a brief stare that made it clear that arguing would accomplish nothing as he continued to send the taser's power through Caldwell's body for another few seconds until he turned it off, leaving the Daedalus commander weakly groaning in pain.

"Colonel Caldwell?" John said as he looked at the man before him.

"Yes..." the man gasped, looking weakly around him, grimacing at the pain in his body from the taser assault.

"Good," John said, stepping back and nodding to Sumner. "Your cue now, Sumner; I'm out of here."

Before Sumner could even open his mouth to protest, John had turned around and hurried out of the conference room, leaving Elizabeth and the colonel to simply exchange brief glances before Sumner crouched down alongside Caldwell.

"We're running out of time, Steven," he said, looking urgently at his Daedalus counterpart. "We need the ZPM access code; can you tell us what it is?"

A couple of hours later, Elizabeth stood silently on her balcony, staring reflectively out at the sea before her.

In the end, she couldn't deny that things had worked out a lot better than they might have done. Thanks to the access code they'd acquired from Caldwell's Goa'uld, the ZPM failsafes had been restored in time for them to safely activate the cloak and leave the distress beacon on the continent to give the impression that the signal had merely been a last remnant of Atlantis that had activated by sheer chance rather than deliberate action, and Caldwell's Goa'uld had been safely extracted from him by Hermiod using the Daedalus transporters.

The only problem with the current situation, in Elizabeth's opinion, was that Sumner's already-shaky opinion of John had been further damaged by his perceived-excessive treatment of Kavanagh; the fact that Kavanagh had turned out to be innocent after John had temporarily dislocated some of the scientist's limbs- particularly given that he went on to shoot the man, albeit just to stun him- did little to convince Sumner that John could be trusted as anything other than a potential rogue element with an unpredictable temper.

The fact that she wasn't that concerned about it herself was actually the most worrying thing about it all; when had she reached the point where she was that willing to excuse whatever John did regardless of how... brutal it was?

He might not have actually caused permanent harm to Kavanagh, but he'd still resorted to methods that she wouldn't have condoned under normal circumstances; what was it about John that inspired so much... faith... that he was a good person when she constantly saw him display such a casual attitude towards physical violence with such limited- practically non-existent- knowledge of the history that had led him to assume his current role?

Had her time on Atlantis changed her so much that she considered what John did... acceptable?

Great... Elizabeth groaned. Here I am, a whole galaxy away from Earth, having almost completed my second year of command, and now I start questioning my judgement about my reliance on this guy...

Maybe Sumner was right; maybe John was too unpredictable to be allowed the kind of free reign of Atlantis that he'd enjoyed so far...

Capturing and containing him for questioning about Atlantis might be an extreme response, but maybe she should consider trying to talk him into maintaining a more... active contact with the military personnel of the city, rather than just his current role of dropping in to help out when he wanted to how he wanted to...

It would be the smart thing to do; John's actions in interrogating Kavanagh, no matter what kind of suspicions they'd had about him, had crossed a line that Elizabeth had always promised herself nobody would be permitted to cross in Atlantis...

So why did she still feel so reluctant to judge John based on his more ruthless moments?

Chapter End Notes: 2: Next chapter jumps- with looks at the intervening episodes, I assure you- to one of those episodes that I'm sure all ShWeir fans enjoy; the Phantom-ised take on "The Long Goodbye"...

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