Ever since John had returned to Atlantis as the new head of the city's military forces, their approach to searching for the city's secrets had been significantly altered. While John wasn't able to give them all the answers all of the time, with most rooms having been locked for the sake of security and caution rather than because he really knew that their contents were dangerous, he was still able to give them a fair amount of information about the city's secrets that they would have never known before, starting with him providing them with some of his surplus ZPMs to bring the city up to full power and progressing from there. While some members of the IOA had objected to John not disclosing the location of his ZPM storehouse, John had neatly deflected their arguments by pointing out the benefits of long-term secrecy in this situation, and nobody had been able to legitimately object to his argument that keeping the ZPMs' location secret would keep them much safer.
It was still too early to offer a definite opinion, but she had to admit that so far operations in Atlantis had been far smoother than they had been before. With John making a genuine effort to connect with his new staff as opposed to Sumner's professional detachment, the new recruits were complimenting the comfortable nature of Atlantis, even if a few of the returning military staff had expressed some uncertainty about what he had done in his private time in the previous two years. Satterfield in particular seemed to have developed a sibling-esque bond with John, treating him warmly without any sign that she was interested in more or judging him for his past.
She just wished that she could feel as good about that as she did; it was completely irrational to feel that jealous about the idea of John having more friends than her…
When she looked up and saw that John had vanished from the area where he had been standing earlier, she initially dismissed it as nothing; it was a big hall and John had a lot to deal with in his new role, so he was naturally trying to take in everything. It was only when she looked around the hall a few moments later and still couldn't see John that she began to get anxious. She had mixed feelings about John's protective nature at times- it sometimes seemed as though he felt that she couldn't be trusted to take care of herself- but she knew that he took his responsibilities seriously even before they became part of his official job; he wouldn't leave her at something this public on only his first trip away from Atlantis.
Glancing around to make sure none of the Rheans were paying too much attention to her, Elizabeth moved off to a corner of the room and sat down, conspicuously taking a drink and toying with it while waiting for other members of the expedition to pay attention to her. Eventually, McKay and Carson moved over to join her at the table, the two doctors looking uncertainly at her as they sat down.
"Something wrong?" Carson asked.
"John's missing," Elizabeth said.
"Missing?" McKay repeated. "It's a big hall with a lot of people in it-"
"I know what John looks like, Rodney; I would have seen him," Elizabeth said firmly; she couldn't fully explain how she could be so certain of that, even to herself, but she knew that she was telling the truth. "If he's not here, where he could be?"
"Well, I know I talked to him a little while ago; he was just… there…" Carson said, indicating the same area where she had last seen John; at least she could be sure that John hadn't gone far if he was sticking around one area.
"Have either of you seen him since then?" she asked, glancing around the area in case she'd missed something; she was still adjusting to seeing John's 'real' face after so long recognising him only by the mask- in a strange way, she saw his new face as just a variation on the original mask- but she felt sure that she would have seen him by now…
Her eyes fell on a door near where John had last been seen, and she quickly got up from her chair to take a closer look. Hurrying through the crowd, she managed to sidestep most of the Rheans' attempts to talk to her while the two doctors followed behind her, only briefly registering Teyla and Ronon coming over to join her as she walked before she reached the door.
When she opened the door and saw nothing, she briefly hoped that she'd made a mistake, but that hope was dashed when she saw marks on the ground; she might not be a professional tracker, but those were definitely drag marks. Turning around, she was saved from asking for help when Ronon crouched down to examine the marks more closely.
"What is it?" she asked the former Runner.
"Something was dragged away from here," Ronon said, taking a moment to more thoroughly assess the marks before he looked back at her. "Something the size of a human male… who was out here?"
"John," she replied, knowing that Ronon would know who she was talking about; the Pegasus natives might have come to recognise that certain names were more common than others back on Earth, but there was only one 'John' she'd identify by that name alone.
To Ronon's credit, despite his obvious discomfort with the man who had once just been the Phantom, he simply nodded at that information before he turned his attention back to the ground. Crouching down, he held out one hand to halt the others from moving forward as he ran his fingers across the upturned dust before him, until he picked something up.
"This look familiar?" the Runner asked, as he handed Elizabeth a small piece of something she recognised immediately.
She hadn't seen many details of John's 'disguise' beyond the 'before' and 'after' images, but she was fairly certain that nobody else at this party would need to be wearing this kind of false skin, and John would never remove it on his own outside of Atlantis, which meant that something had gone wrong.
"We need to move quickly," she said, looking urgently at the group around her. "Ronon, Teyla, get to the gate as fast as you can; it's the only way off-planet, and if someone took John, it's possible that they haven't managed to move on yet."
"Done," Ronon said, before he turned and ran towards the courtyard where this planet's Stargate was located, followed closely by Teyla. With that issue dealt with, Elizabeth turned and marched back into the hall with Beckett and McKay, taking a moment to beckon Major Lorne over to join her before heading for the mayor.
"Doctor Weir?" the mayor said, looking at her in surprise. "What is-?"
"My chief military officer has just gone missing, and I have reason to believe that he has been abducted," Elizabeth said, looking firmly at the other man, the new major's presence behind her giving her a degree of confidence as she made her statement. "Aside from everyone here, who else knew that we were coming?"
"Only a few of our mutual trading partners," the mayor replied; his shocked reaction to the news at least confirmed that he hadn't been expecting this news, but she had to assume that he had some idea of who could have been this even if he hadn't planned for it. "The Genii in particular seemed interested; I believe that-"
"That's it," Major Lorne said, looking firmly over at Elizabeth. "It's the Genii."
"You believe that the Genii have captured your military leader?" the mayor said, looking at Major Lorne in surprise. "I understood you were allies-"
"We are now, but back when we first met, there were… difficulties," Elizabeth explained, fighting down her initial discomfort as she looked at her local counterpart. "I have no reason to believe that Ladon Radim would have done something like this, but there are… other factions among the Genii who wouldn't be as forgiving."
She didn't like to consider the possibility that Ladon could have betrayed them, but John had killed nearly sixty of their people during their attempt to take Atlantis. Ladon might be willing to forgive that as a past grievance, but that wouldn't stop some people from wanting to get revenge now…
She reminded herself that none of the Genii could know that John Sheppard was also the Phantom who had killed so many of their people during that last raid, but that could only give her so much comfort; even if they didn't recognise him, once they got past that make-up, he was going to be in serious trouble.
"Damnit…" John muttered, shaking his head in frustration as he opened his eyes. "Chloroform… who the hell does that to people any more?"
As he turned his head and realised that he was sitting in a cell, he cursed in frustration at his situation, only to realise that things were even worse when he felt the breeze against his damaged skin.
Whatever had happened to him, his current captors had removed his disguise, which meant that he was now extremely vulnerable and dealing with people who probably saw him as a feral beast who'd tear them apart at the slightest provocation…
"Hello?" he called out as he walked over to the cell door, not holding out much hope of a response but stuck for any alternatives. "Anyone there?"
"You're wasting your breath," a voice said. Glancing in the direction of the voice, John saw a small barred window in the wall, leading to a heavily-shadowed room that was almost certainly another cell.
"Didn't know I had company here," John noted, walking over to the cell.
"There is no escape," the voice said.
"There's no intended escape; that's not the same thing," John corrected, looking through the window to try and see his cellmate. "I know I probably look like something that should be in a stronger cage, but I'm not… y'know, a Wraithspawn…"
"I know," the voice said.
"You do?" John said in surprise. "How?"
"You were unconscious for too long and were too calm upon awakening," the voice replied. "A Wraithspawn would have awoken earlier and attempted to escape by breaking down the doors."
"Ah," John said, deciding to chalk that discovery up as a win and take it from there. "Good to know that someone has some sense here…"
"You doubt our captors will know the difference?" the voice asked.
"Let's just say they already have more reasons to dislike me than even they know of; the face probably just makes it easier for them to hate me," John elaborated, straining his eyes to see something in the gloom; he'd grown too used to the additional vision features of his mask. "How long have you been down here?"
"Many years," the voice said solemnly, accompanied by a clanking sound that made John think of chains.
"How many years?" he asked. "Five? Ten?"
"It no longer matters," the prisoner said solemnly.
"That long, huh?" John noted, trying not to feel too apprehensive at the thought that this prison was that good; it wasn't like many places in the galaxy had Atlantis's resources, after all. "What did you do to get here?"
"I merely allowed myself to be captured alive," the voice replied.
"Same here," John said, turning his attention back to the cell around him; with only his new dress uniform, he lacked most of the weapons he was used to packing in enemy territory, but at least he had some external options this time around. "Look, I'm sure that my people are looking for me; when they find me, we can-"
He was interrupted when a door opened and guards walked in, one of them walking up to his cell door and aiming a gun through it while another one opened the cell.
"Don't move," the man said, in a loud, clear voice that John would have normally associated with someone trying to tame a dangerous animal. "Stay still. Do nothing."
Under other circumstances, John might have made a joke, but with the guard clearly operating on a hair trigger and a large gun pointing at him, all he could do was raise his arms and wait as the other guard walked into the room, attaching handcuffs to his wrists as he was made to place them behind his back.
As he was marched out of the cell, he wondered if he should be more or less concerned about the fact that these people obviously thought he was some deranged animal rather than a self-trained soldier; he might be able to outsmart them if they were underestimating him, but it also meant that they would be keeping a really careful eye on him…