In the end, however, all this work didn't change the fact that Elizabeth still had to get around the fact that she had yet to come to any decision about her issues with the Phantom.
The events of the Trust's attempt to blow up Atlantis might have left her questioning his methods, but that didn't change the fact that he'd still come through for them when it really counted; she could hardly question whether he'd prove to be a danger to them at some point in the future when they'd spent almost two years here so far and everything that he'd done had only been to their benefit...
What was it about John that constantly left her feeling as though he had a good reason for even his most questionable actions? She tolerated Ronon's occasional moments of brutality- she was fairly certain that he would have been ready and willing to use physical violence to continue the interrogation of the now-departed Kavanagh if John hadn't been available-, but that was because she knew what had happened in his past to drive him to that point, and even then she couldn't help but feel wary about him; with John...
She might be uncertain about his past, but somehow, she couldn't imagine what she'd do if he proved to be dangerous to the rest of the expedition simply because she couldn't conceive of a situation where he would be dangerous to them.
Even when they found further reports of what he'd been doing on other planets before their arrival, they seemed to support her idea of John as a man who recognised when taking no action was more helpful than taking the wrong one. The recent incident with the Lord Protector, for example, had included the former 'prince' of the planet mentioning that 'the Phantom' had shared the expedition's objections to the current social structure, but he'd left them alone after failing to change their minds about anything.
It might have been her own... friendship... towards him influencing her assessment, but personally Elizabeth couldn't help but see that as an encouraging example of John's attitude; when he'd failed to make the Lord Protector change, he'd left the situation alone so that the people could still be protected (The expedition might have made some changes themselves, but there was a difference between being an extremely skilled fighter and having the kind of resources possessed by the SGC available to you)...
"Doctor Weir?" Chuck said from the door, prompting Elizabeth to break off her train of thought- something she had to admit was probably for the best; she was starting to risk approaching dangerous territory if she continued thinking for much longer- and look up at Atlantis's head 'gate technician. "We've just received word from Colonel Sumner's team; they've found something that you might be interested in."
Pushing the forms before her off to the side, Elizabeth stood up and followed Chuck, hoping that whatever she was about to learn would at least prove interesting; after everything else that had been going on in Atlantis recently, they could use a decent intellectual puzzle rather than an obviously dangerous one...
As he sat in his usual 'resting place' in the Atlantis repair tunnels- as much as anywhere in the tunnels could be said to be somewhere that he could rest; they weren't exactly built for long-term habitation even without the fact that he had to constantly monitor what was happening in the main city in case one of Sumner's search parties ever came close to finding his current location-, John silently listened to the current conversation taking place in the lab, Elizabeth's radio having been activated after she'd left her office so that he could be aware if anything turned up that he should know about.
He had to admit, the concept of these 'stasis pods' that Sumner's team had discovered was enough to intrigue him just as much as anyone else, and the expedition could definitely use allies with the Wraith still building up power in the galaxy, but he couldn't help but feel at least slightly uncomfortable about the whole thing; encounters with the likes of the Genii and Halcyon didn't exactly encourage you to hope for the best when dealing with advanced civilisations in this galaxy.
Of course, Caldwell's presence on Atlantis while Daedalus was away didn't exactly make him feel particularly comfortable, although that could just be because it was the first time Caldwell had spent any kind of time in the city since he had his Goa'uld extracted. He respected the man's desire to make up for what the Goa'uld within him had done before it was exposed, but that wouldn't stop him being a bit on-edge; it might just be because of his limited knowledge about them in the first place- the Elizabeth he'd first met had been more focused on telling him about what he might confront in the Pegasus galaxy rather than talking about what the SGC had dealt with back home, and he hadn't had the time to find out anything more detailed about them since then-, but he just found it hard to be comfortable around the guy...
"...alive- barely," Doctor Beckett's voice said, drawing John's attention back to the conversation taking place in the lab; he couldn't see the location himself- there hadn't been time to move to that area and it didn't sound like anything was going to happen to Elizabeth there that required her attention-, but it sounded like they'd opened the pod they'd discovered already. "It appears we found her very near the end; all the major organs are shutting down."
"How long was she out there?" Elizabeth asked, her voice a low, astonished hush.
"There's no way to tell for certain," Doctor Beckett replied.
"So she could be an Ancient?" Elizabeth asked.
"Uh, the pod design makes me doubt that," McKay replied, evidently sceptical, prompting John to dash that possibility from his mind; McKay might be arrogant, but he knew his technology well enough to know whether or not something was Ancient.
"It's a shame she can't speak with us," Elizabeth continued. "Just imagine what she could tell us about her people and about what happened to her..."
After a moment's pause, John heard a sound like something activating, followed by the sound of someone falling and McKay calling out Elizabeth's name.
"Medical team to Lab Three, stat!" Beckett called out, confirming John's worst fears but simultaneously leaving him with nothing to do but sit apprehensively in his small corner of shaft as he listened to the subsequent hustle as Elizabeth was hurried off to the infirmary, John only able to briefly register the rest of the panicked confusion taking place in his ear as he waited for some sign that Elizabeth was all right.
She had to be OK... she had to be fine... he couldn't have been so careless as to let her get killed in a stupid accident like this... it was just a damn pod, just a simple routine thing...
"This is not my fault," McKay's voice protested, the Canadian's annoying tone serving as a strange source of comfort for John as they drew him out of the panic that had been dominating his thoughts since whatever had happened to her had happened. For all of McKay's faults, he wasn't insensitive; if he felt that the time was right for him to be talking like that, then Elizabeth was probably past the worst of whatever had happened to her.
"We were all there, Doctor; we know what you were and weren't responsible for," Sumner said, his tone inspiring more reassurance in John than McKay's. McKay might have confirmed for him that Elizabeth was past the worst of what was happening, but Sumner's tone made it clear that he was willing to make sure McKay recognised that he'd been an idiot to let Atlantis's leader be in such close proximity to an unknown alien device...
"She's coming around," Beckett said, giving John a brief moment to sigh in relief at the sound of footsteps as people moved to (Presumably; he'd been so focused on listening for news of Elizabeth's condition that he hadn't been able to bring himself to head to the medical bay to check on her himself).
"Are you all right, Doctor Weir?" Sumner asked.
"Doctor Weir is fine," Elizabeth's voice replied in a slightly bland tone.
Instinctively, John found himself tightening his grip on the gun he hadn't even realised was now in his hand; even without the fact that he'd been thinking about the Goa'uld earlier, that choice of wording definitely didn't sound entirely encouraging...
"I take it from that comment that you are not Doctor Weir?" Sumner said, a faint sound suggesting that he was arming a weapon while trying not to be obvious about it.
"She was simply overcome by the effects of the imprinting," Elizabeth's voice replied with a nonchalance that John himself wasn't feeling at this point.
"Security team to the infirmary," Caldwell said, along with a slight tap that sounded like he was activating his radio (Not that John could know for certain; he was currently 'tapping' into Elizabeth's radio rather than Caldwell's, after all).
"That's not necessary, Colonel... Caldwell," Elizabeth's voice said reassuringly. "She is... merely harbouring my consciousness."
"And you are?" Sumner asked (John thought he heard McKay muttering 'again', but concluded that it wasn't important; what mattered right now was what had happened to Elizabeth now, not pondering the similarities to things that had happened in the past).
"I am Phoebus," 'Elizabeth' replied. "We are a race of explorers. On our journey home our vessel was attacked."
"By the Wraith?" Caldwell asked.
"Yes," Phoebus replied (John couldn't think of her as Elizabeth even if the voice was the same; it wasn't Elizabeth where it really counted). "We were forced to abandon ship and launch our life pods. If this has happened to me, then I've been adrift for some time and the pod has determined my body is beyond resuscitation."
"You're quite correct," Beckett said apologetically.
"Then, for all intents and purposes, I am already dead," Phoebus said, her tone a simple, direct one that gave no indication about her feelings on the matter.
"I'm sorry," Beckett said.
"So am I," Phoebus replied simply.
"Getting past that issue, would you mind clarifying what happened to Doctor Weir when she began... harbouring your consciousness?" Sumner asked.
"She is here also," Phoebus replied, even if that statement did nothing to assuage John's concerns about what had happened to Elizabeth in this whole mess.
"And I suppose you'd like us to take your word for that?" Caldwell asked, neatly voicing John's own concerns about the current situation; after their experiences with Caldwell's Goa'uld, anything that used another person's body like its own was unlikely to easily win their trust.
"Would you like to speak to her?" Phoebus asked nonchalantly.
"If you can," Sumner replied, followed by a brief pause before Elizabeth sighed again.
"Doctor Weir?" Caldwell's voice said once again.
"Oh!" Elizabeth said, her voice now demonstrating more emotion than Phoebus had previously. "Oh, it's OK, Carson, I'm- I'm fine."
"Doctor Weir," Sumner said, "I have to inform you that-"
"I know," Elizabeth replied casually. "Her name is Phoebus."
"You seem remarkably... sanguine about all this," McKay put in, addressing John's obvious concern about this; after the Goa'uld, he'd have been very uncomfortable with anything living in his head.
"Well, the imprinting will only last a matter of hours," Elizabeth clarified, before she continued. "The other pod – Phoebus urgently desires to be here when we bring the other pod back to Atlantis."
"Why?" Sumner asked.
"She believes it's her husband," Elizabeth responded, her voice sounding almost amused at the prospect.
"Husband?" Caldwell repeated, John only just stopping himself repeating the word himself, his mind distracted from his previous thoughts of Elizabeth's odd word choice; something about that sentence- and, now that he thought about it, the tone of the last one- hadn't sounded quite right...
"He escaped the ship- she's certain of it," Elizabeth explained, sounding almost like a giddy schoolgirl as she spoke (John was definitely making sure she had a check-up after this; Elizabeth wasn't meant to act that way, she'd always been so professional...)
"And, uh..." she continued, laughing briefly as she spoke. "The rush of emotion is... it's overwhelming."
Even knowing that it wasn't really Elizabeth feeling the emotions that she was talking about- and that he had no actual right to feel that way- did little to help John quash the sudden stab of jealousy he felt at that last comment; the prospect of another man inspiring that kind of... emotion... in Elizabeth was something he didn't like to consider in depth.
"Actually," Elizabeth continued after a momentary pause, "on the topic of emotion, Phoebus has a favour she'd like to ask you, Colonel Sumner."
Once again, John fought back an irrational jealousy as he processed the implications of what he was hearing; he had no right to have any kind of say in who Elizabeth did or didn't... have feelings for... no matter whether or not he thought that Sumner was a git without any real improvisational talent...
If she was happy, he could accept that; that was all that mattered...
"As I understand it," McKay said an hour or so later as they stood in the lab with Phoebus's pod once again, the pod containing her alleged husband now in the room as well- taking advantage of the time needed to pick up the pod and bring it back, John had crawled over to a tunnel near the room so that he could make sure the transference progressed safely, even if he was already resolved to depart if anything... happened... between them-, "the beam that hit Elizabeth was part of a failsafe feature built into the pod system. As cellular failure progressed, the pod stored her consciousness in a sort of, uh... flash memory."
"Why?" Caldwell asked. "I mean, what good is the technology if the effects are temporary?"
"A black box equivalent seems the most obvious possibility," Sumner speculated. "If the bodies themselves can't be recovered, the minds would at least be able to report what happened to the ship and allow the rescue team to determine what had happened."
"A human flight recorder..." Caldwell muttered, shaking his head as he studied the pods. "That's pretty dark."
"Maybe, but it's also useful in times of war," Sumner pointed out.
"As well as for giving two survivors the chance to say one last goodbye, mmm?" McKay added, smiling at Sumner just as Doctor Beckett arrived, Elizabeth/'Phoebus'- John had no way of knowing who was in control at this point- sitting in a wheelchair in front of him as her eyes automatically focused on the pod before them.
"Are you sure she's up for this?" Caldwell asked as Elizabeth/'Phoebus' got out of the chair to step closer to the pod.
"Physically, she's perfectly fine," Beckett said (John wished the guy had said that it wasn't OK; even if Elizabeth wasn't going to be the one doing it consciously, her body was still going to... do that... with someone...). "Besides, Elizabeth wouldn't take no for an answer."
"Love is a powerful thing, Carson," Elizabeth said in a low voice as she studied the pod.
"You're a hopeless romantic, aren't you, Doctor Weir?" Sumner said, the other man smiling slightly as he looked at her.
"Well, you're just as hopeless, otherwise you wouldn't have agreed," Elizabeth responded with a smile.
"It was a dying woman's last request, Doctor Weir," Sumner replied with a brief shrug, the slightly nostalgic smile on his face one of the few true signs of emotion John had ever seen the man express. "That's not something you can turn down."
"Besides," Doctor Beckett added, "from what I've been able to determine from going over the respective EEG patterns, I can say with some degree of confidence that this... 'imprinting'... as Doctor Weir's temporary occupant calls it, won't last more than a few hours."
"You can guarantee that?" Caldwell added (John actually found himself agreeing with the other man for what seemed like the first time since he'd first seen him; the last thing he wanted was Elizabeth playing host to a technological 'ghost' on a long term basis).
"A day at most," Beckett confirmed.
"Well, I'm sold," McKay said, looking around at the others before indicating the still-sealed newly-arrived pod. "Shall we?"
Without waiting for a response, he pressed something on his computer tablet and the pod lid slid open, revealing an elderly man in a brown uniform of some kind.
"He's still alive," Beckett said after a brief glance at his scanner, Elizabeth staring at the old man with a slightly tightened expression. "Same as before. Life signs even fainter than the first one. If we're going to do this, we should do it now."
"Take this," Sumner said, unstrapping his pistol and handing it over to McKay. "Whatever else is happening here, I'd prefer it if my body wasn't armed in this situation."
Nodding briefly in acknowledgement, McKay took the offered weapon, Sumner subsequently taking a brief step towards the pod before he turned to look at Elizabeth.
"If anything... happens... between them, Doctor Weir," he began, looking as close to being uncomfortable as John had ever seen the colonel in question, "I want to assure you-"
Elizabeth cut him off mid-sentence as she held up her hand and lowered her head, taking a deep breath before raising it again, this time with a slightly different expression on her face that suggested to John that control of her body was once again in Phoebus's metaphorical hands.
"I promise to be discreet, Colonel," she said simply (John really wished he could put away the mental images implied by that statement; the slightly seductive tone she used at the time didn't exactly help matters).
"Well..." Sumner said, taking a deep breath as he looked at the pod. "See you all later."
With that, he walked up to the pod and leaned over it, a white beam shooting out of the pod to envelop him almost instantaneously, Phoebus subsequently holding out a hand to halt Beckett's attempt to approach the colonel as Sumner swayed slightly unsteadily on his feet.
"Give him a moment," she said, patiently watching Sumner as he stood by the pod, his head lowered, until his head snapped up, his eyes open and automatically fixing onto her.
"Thalen?" Phoebus said, smiling slightly at him. "It's me."
"Phoebus?" 'Sumner' replied uncertainly.
"It's all right; these people recovered our pods," Phoebus replied, as she began to walk around the pod towards Thalen. "We may well be the very last of our kind; these... generous people have allowed us to be together one last time."
"You consented to this?" Thalen asked, looking over at Caldwell, apparently identifying him as the authority figure in this situation.
"One last chance to say goodbye," Phoebus replied with a brief smile. "It seemed... appropriate... to use these bodies for that purpose, given the... relationship between them."
For a moment, John's fists automatically clenched at the implications of what he'd just heard; the thought of Elizabeth and Sumner having the kind of connection that he'd longed to have with Elizabeth for longer than he could even remember...
STOP IT! he mentally berated himself, pushing that thought to the side as hard as he could.
It wasn't worth thinking about things like that; no matter how much he might like to dream otherwise, those thoughts would bring him nothing but heartache and frustration if he ever tried to act on them.
So long as Elizabeth was happy...
"I know this body is different," Phoebus continued, "but I assure you, Thalen, it's me."
With that said, she turned her attention to the others even as she continued to face the man who had once been Sumner. "Is it possible for us to be alone, just for a few minutes?"
"No, absolutely not," Caldwell said. John couldn't help but feel briefly supportive of Caldwell in that moment; even without his jealousy issues, the idea of Elizabeth's body doing something like... this... when she wasn't in control of it...
Even if she'd consented to letting Phoebus remain in control, it still felt like rape to him...
"Don't be so heartless!" Beckett said, looking over at Caldwell with a slightly scolding tone.
"They are two consenting adults!" McKay added in exasperation.
"That's not what I'm concerned about, Doctor," Caldwell said (John just wished he could convince himself that the city's security was all that he'd been concerned about in that moment...).
"The Colonel's right," 'Thalen' said briefly.
"Doctor Weir is in charge of this facility," Phoebus added, looking uncertainly at him.
"I'm just saying, there should be an armed guard just outside the door," Thalen continued.
"Two guards," Phoebus added, her eyes flicking briefly over to look at the colonel. "One in each door."
"I've already taken that precaution," Caldwell put in. "They're right outside."
"Of course they are," Phoebe said, she and Thalen exchanging brief smiles.
Before anyone could stop them, the two leaders of Atlantis- the fact that they were in the leaders' bodies was the only thing saving them from being shot at this point, in John's opinion- suddenly turned and ran towards their nearest doors, McKay's startled yells ignored as Thalen and Phoebus both swiftly rendered the guards unconscious and stole their Wraith stunners, Thalen swiftly taking Caldwell out with his stunner as Phoebus hid behind the other door. The evidently-panicked McKay drew the gun that Sumner had given him and tried to fire at the possessed colonel, only for Thalen to turn and run off down the corridor as Phoebus walked back into the room, her stunner aimed at him.
"You two need some very serious marriage counselling-!" McKay began.
"He's not my husband; he's the enemy," Phoebus replied, confirming John's assessment that there was something else going on here, her tone giving the impression that McKay was an idiot for not realising the truth sooner. "Drop your weapon."
Lacking alternatives, McKay dropped the pistol to the ground.
"Now radio security and tell them everything is fine," Phoebus continued, unaware of John pulling out his gun and shifting it into stun mode as he prepared to exit his small observation point.
It wasn't something he'd like to do, but if it meant stopping Elizabeth's body being used to do something that she herself would never condone...
He aimed his gun at her, his body tenser than it had been when he first began his journeys through the Stargate- even after all the training he'd done there was no way to know how you were going to be able to cope with something as dangerous as what the old Elizabeth had told him about the Wraith-, waiting for the moment when he could shoot her... she'd stunned Beckett for speaking, but he was still all right... McKay was making a transmission to 'confirm' that everything was fine... Elizabeth's body was contained, she wasn't going to do anything...
"Oh, forget it," Phoebus said, casually stunning McKay as he continued to talk incessantly in a manner that wouldn't have convinced anyone, before she walked over to the fallen scientist and took his headset for herself.
"This is Doctor Weir," she said, the same cool authority that had always drawn him to Elizabeth somehow instinctively perverted as she picked up a gun along with her stunner. "Attention all personnel. Colonel Sumner is not, I repeat, not who he pretends to be. If you find him, secure the area and contact me immediately; I'll deal with him myself."
Damnit... John thought to himself as Elizabeth walked out of the lab, leaving him staring in frustration at the suddenly-empty room before him, filled with nothing more than unconscious soldiers and doctors as their possessed commanding officers headed out into a city that had no idea what had happened to them and were equally ignorant of what they were up against.
There was nothing else for it; he'd have to backtrack to somewhere that would allow him to exit the tunnels- his current location was good for taking pot shots at the people in the room but he couldn't have actually entered the room to take a more physical role in things from this point-, and hope that he could find Phoebus or Thalen before they did something Elizabeth or Sumner would regret...