Hi guys! I've been working on this update for a while, trying to get it all into one, but I finally gave up and broke it into two. So you get an update tonight!!

Happy Reading!

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Misbegotten Cont.
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It was two weeks before Elizabeth returned to Atlantis. In that time everyone had their hands full. Kai and McKay spent most of their waking hours working on the ships. Kai often rotated between the two depending on where she was needed.

She and John had only seen each other in passing as his whole focus had been setting up the transitioned wraith on a planet. The story they came up with was that the men had caught a virus that made them lose their memories and were in quarantine. So far it seemed to be working and Beckett had remained on the planet with the wraith to help them through the transition so they could learn to administer the drugs themselves.

The Asgardian ship with Weir and Woolsey arrived in the middle of the night. Sheppard and Lorne was standing with their hands behind their back as they waited for them to beam Elizabeth and Woolsey into the Atlantis gate room. Sheppard had warned Lorne of the IOA investigation and Lorne was prepared for a formal reception, standing at attention.

When they appeared John's eyes ran over the shorter man standing beside Elizabeth. Despite the late hour he was dressed in an impeccable suit and carried a briefcase. Elizabeth only had one bag over her shoulder, but three others appeared beside Woolsey. Sheppard and Lorne shared a look before Elizabeth cleared her throat bringing their attention back to her and Woolsey.

"Mr. Woolsey, may I introduce-" she began but was interrupted.

"Lietenant Colonel John Sheppard, military leader of the expedition, and team leader
of Atlantis Reconnaissance  Team 1," Woolsey said, holding his hand out.

John shook it, with a small frown. The disrespect of interrupting Elizabeth immediately put his teeth on edge. "This is-" he started to say, but Woolsey interrupted him as well.

"Major Evan Lorne," Woolsey said shaking his hand. "Second in command of the military operations of the expedition, and team leader of Atlantis Reconnaissance Team Two," Woolsey said with a curt nod.

"That's right," Lorne said, his eyes flickering from Elizabeth to Sheppard.

"Major Lorne will show you to your quarters," Sheppard said, gesturing up the stairs behind them.

"That would be excellent," Woolsey agreed with a sharp nod. "I'll want to get started early tomorrow morning."

Sheppard pressed his lips together grimly and nodded. "Course."

"My bags..." Woolsey dragged off, looking at Lorne expectantly.

Lorne's lips pressed into a grin smile. "Got 'em," he said with forced brightness as he shouldered the three bags. "This way," he said and he led the way down the hall and out of sight.

Weir gestured for Sheppard to follow her into her office. He closed the door behind him as she stepped up to her desk and shuffled through the massive pile of memos, requests, and files that had accumulated while she was gone. While Elizabeth was always confident in Sheppard's ability to lead, administrative paperwork had never been his strong suit and she had no doubt he hadn't touched anything on her desk since she had left.

John dropped down into one of the chairs opposite her desk. "Good to have you back," he said.

Elizabeth shuffled through a few more papers before looking up at him. "It's good to be back," she exhaled and dropped into her desk chair, resting her palm against her cheek. "Give me an update. What's been happening?" she asked. Although she was exhausted, she needed to get up to speed as quickly as possible. She felt like there were only a few hours until Woolsey began tearing their lives apart and she didn't want to be caught flat footed.

"Things have been pretty quiet," John said with a shrug. "Almost everyone we can spare has been working on the Daedalus or the new Hive. Beckett is still on M8G-352. He is working to get the wraith independent enough to administer the drugs to each other so we can pull out. Maintaining the settlement there is straining resources and personnel."

"And things there have remained peaceful?" Elizabeth asked.

John shrugged. "Seems to be."

Elizabeth nodded thoughtfully. That particular decision was sure to come up in the interviews with Woolsey. She still wasn't confident it had been the right decision for the expedition, but she couldn't have lived with any other outcome.

"So, what can we expect from Mr. Charming?" John asked jerking his chin towards the door. So far his first impression of the IOA agent wasn't a favorable one. He was all too familiar with investigatory committees, although he wouldn't be surprised to hear this was one of Elizabeth's firsts. She wasn't really the type to get caught breaking the rules.

Elizabeth sighed. "I'm not quite sure. The IOA isn't happy with my decisions regarding the alliance with the Wraith and Mr. Woolsey is here to 'simply get to the bottom of things', according to him."

"He seems great," John said sarcastically.

"Well, he's going to be digging into every one of our closets trying to find a reason to have us fired," Elizabeth drew in a steadying breath. She needed to have this conversation with John, it was long overdue, but that wouldn't make it any easier. There was only one thing she could think of that could be an issue. "I have to know John, is there anything for him to find?"

"Of course not," John snapped indignantly. He paused a minute and frowned.

"What?" Elizabeth asked suspiciously.

"There's been a lot of missions, a lot of decisions made, I'm sure if he goes back far enough he'll find something the IOA disagrees with," John said with a casual shrug. He had faced his fair share of misconduct evaluations, including one court marshal that hadn't stuck. The IOA just didn't scare him that much.

Weir arched her eyebrows meaningfully. Clearly unimpressed by his casual response. She knew John's background better than most people. She was well aware of his history of not taking authority very seriously, but she didn't appreciate his cavalier attitude when it came to this IOA investigation. This was her career on the line.

She drew in a breath and braced herself for the question she had to ask. "And if he asks about Kai?"

John opened his mouth to respond but froze. He couldn't honestly say there was nothing going on between them anymore. They had moved beyond the gray area they had been stuck in for so long and he wouldn't lie about it. He refused to treat Kai like a dirty little secret. She meant more to him than that. He closed his mouth and looked away.

"Jesus John," she snapped shoving herself to her feet. Elizabeth paced aggravated lines behind her desk. She had known something was going on, she should have trusted her instincts.

"I was going to tell you about it," he said defensively.

"When?" She snapped. "When exactly were you going to tell me the military commander of my expedition is fraternizing with an alien super assassin from another galaxy!"

"There has been no fraternizing," John said, his voice low and tight with his barely contained anger. John's temper snapped and his eyes narrowed dangerously. "I respect you enough to tell you before things became more serious. I respect you, but don't ever call her that again," he snapped.

Elizabeth stopped and stared John in the face. "That's what she is, John," Elizabeth said more gently. "You'd be risking your career for her."

John clenched his jaw and fought to contain his anger. "Threatening to fire me over this? That's a little harsh don't you think? I haven't broken any rules. She's not in the military or technically even part of this expedition. She doesn't even get paid."

Elizabeth narrowed her eyes at John. "I asked you point blank after the morning she was in your room and you assured me nothing unprofessional had gone on. Did you lie straight to my face?" It was the one thing she needed to know. The one thing she couldn't get past. If John had been lying to her they couldn't work together. She had to be able to trust him.

"No!" John snapped. "Nothing," he gestured uselessly in the air. "-like that has happened."

"Then what John? What has happened? And when did this grand romance start?" Her temper made her sarcasm even more biting than usual. She needed to trust John, and this had blind sided her.

John tightened his jaw. There was part of his brain that recognized he needed Elizabeth on his side. But the other part was fiercely protective over Kai and their fragile new relationship. He took a deep breath, forcing his temper back under control. Elizabeth was a hopeless romantic, and she liked Kai. If he couldn't convince her to support him, no one would and this would all be over before it began.

"We've kissed, had a couple dates. Nothing more. It started after I thought she was dead...when the Genii took her and Lorne," John said stiffly. "I spent forty-two hours believing she was dead, I decided I was done waiting. I don't want any regrets."

"And how long was this going on before that?" Elizabeth asked pointedly. "Clearly these feelings didn't just pop up out of no where."

"I don't think that's your business. No rules were broken," John said in a steely tone.

"If you think my questions are harsh how do you think Woolsey, or General Hammond, or General O'Neil are going to respond. I might lose my job over this. I think that makes it my business. Were you at least smart enough to not get caught on film that Woolsey might find?"

"I don't know when it started," he said honestly. "When we were looking for Aidan," he shrugged. "Maybe sooner."

Elizabeth stared hard into John's face. "You're serious about this," she said in disbelief. John had always seemed like such a playboy, leaning hard into that stereotype every chance he got. The amount of women who threw themselves at him was staggering. She had never imagined this could be anything but a passing infatuation. Kai was unattainable and exotic, nothing more. Exactly the type of woman someone like John would want right up until he had her. She respected John as a military leader, but he would always be a skirt chasing playboy in her mind.

John didn't respond. He tightened his jaw and met Elizabeth's gaze unapologetically. Elizabeth could think whatever she wanted. He wasn't going to apologize for his feelings.

Elizabeth sighed, cupping her forehead. "She's from a different galaxy."

"You think I don't know that?" John demanded. "You think you can come up with any reason or excuse for us not to be together that I haven't already thought of? Cause if you can by all means," he said gesturing to her. "It's been almost two years Elizabeth. I think I know what I want."

"This isn't like Teyla or Ronon, who are just from here. She isn't even human John!" Elizabeth exclaimed in frustration.

John's eyes hardened and Elizabeth knew in that moment she had pushed him too far. John was always so easy going it was easy to forget the steely soldier that hid beneath the good humor and jokes.

"It doesn't make her any less of a person," John said coldly. He was done. It was clear he wasn't going to get through to Elizabeth and she wasn't about to give an inch either.

Elizabeth pressed her lips together. "I think you should take some time, a week, and think this through John. I don't want you to make a decision you will regret because you're being stubborn."

John stared hard into Elizabeth's face. "There's nothing to think about," he said and he stalked out of her office.

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Kai was exhausted. She had been burning the candle at both ends trying to get the two ships repaired. Beaming back and forth between Radek on the Daedalus and McKay on the Hive ship. The Hive was coming along faster than the Daedalus, the organic hull ensured it healed itself while they were fixing other systems. It made a world of difference while the Daedalus sat like a lump of scrap on the south pier while Hermiod argued and offended everyone but her. She wasn't sure what she had done to earn the Asgardian's respect, but he seemed to tolerate her better than anyone else.

Kai stepped under the shower spray with a groan. Despite the late hours she had gone to the gym after work. It was nearly the middle of the night, but it felt good to stretch her body. She hadn't been sparring much and recognized she needed to get back at it to keep her skills sharp. She frowned and froze as she was reaching for the conditioner bottle. Her chest felt suddenly tight with...there were too many emotions to separate. All she could think About was John.

She quickly rinsed out the last of her hair, intending to go find him to make sure he was all right. She turned off the shower, and the door chirped, letting her know someone was there. She knew without a shadow of a doubt it was John. She quickly dried off, and wrapped a towel around her hair. The door chirped twice more in quick succession and she grabbed a robe, tying it around herself as she strode across the room.

The door slid open and John stepped inside before she could say anything. He waved his hand over the door, closing it as he moved towards her, pulling her into a passionate kiss. She could feel the storm of his emotions in her chest and when he reached for her it felt like there was electricity running between them. John wrapped a hand around her hip, pulling her towards him and gripped the back of her neck so he could control the kiss.

Kai responded with equal enthusiasm and when his fingers slid up, under the edge of the towel he pulled it free, spilling her wet wavy hair down her back and into his hands. John's kiss was passionate but there was an edge to it. One Kai didn't entirely understand but she wasn't about to back off.

John dropped his hands to her hips and lifted her up. Kai wrapped her legs around him and he turned them, moving them towards the long dresser, pinning her against it. John was painfully aware Kai was naked under the robe that was becoming looser by the second. One shoulder dropped, leaving the long line of her neck and shoulder bare. His lips traveled down her neck and over the skin of her shoulder that was still damp from the shower.

Kai moaned and locked her legs around John's lean hips, pulling him closer.

John groaned. Kai felt so good and every part of him wanted this, but this wasn't why he was here. They had to talk. It took every bit of self control he had to pull back and rest his forehead against hers. He was panting as he fought to get himself together.

"I'm sorry," he said in a tight voice. He moved slowly and deliberately, lifting the edge of her robe up so her shoulder was covered once again.

"You don't have to be sorry," Kai said breathlessly. But instead of feeling more settled she could feel the storm of John's emotions rising and becoming more unstable. It was incredibly rare for her to feel any emotions through the Bond, the fact that she was continuing to pick up from him was telling of his mood.

Kai reached up and cupped the sides of his face, forcing him to meet her gaze. "What happened?she asked gently.

John shook his head and moved his hands so they rested on her waist as their foreheads touched. It had seemed like an odd gesture when they first grew close, but now John found it soothing. He exhaled. He owed Kai an explanation. He hadn't intended to just show up and start something, he really had intended to talk, but when the door opened and he saw her it was like he couldn't breathe unless he touched her. Like he might lose her.

"Elizabeth knows about us," he said quietly, stepping back to give Kai room.

Instead of reacting, Kai's face shut down as her thoughts began to race. She had expected John would tell Elizabeth eventually. She just hadn't expected it so soon, when things were still so uncertain between them. It also left her taken aback. The fact that John has chosen to tell Elizabeth meant this was serious for him.

She cleared her throat delicately. "I take it, it wasn't a positive conversation."

John snorted and started pacing agitatedly. "To say the least. She kept telling me I needed to think of my career and calling you an alien. Can you believe that?"

"Well John," Kai said gently. "I am. I'm not human," she reminded him.

John pulled back with a scowl on his face.

"Look," Kai said shifting her weight. She was uncomfortable with vulnerability and she was about to lay herself bare, but she owed John at least that much. "I think maybe you should think about all the things Elizabeth said."

John opened his mouth and she reached up and touched his face. He froze under the familiar contact. Kai initiated things between them so rarely, he recognized them for the gift of trust they were.

"I know you don't see it that way, but with this agent here investigating it's probably better for us to keep our distance anyway. As much as it hurts when people throw it in my face, I'm not human. And if Elizabeth is right, and you would be risking your job for this..." She dragged off and shrugged, not sure how to articulate what she felt. All the vulnerability she felt however was evident in her voice.

John was ready to argue, ready to rage but when he looked into her eyes he could see just how badly she wanted this and that in her own way she was trying to protect him too.

"I don't need time," he said and he reached up and his fingers glided over her skin. "I know how I feel."

"But there are other people who depend on you, and attachment to a Mortii could strain some of those relationships."

John's jaw tightened. He didn't like it, he didn't want space. He wanted the opposite and he damn sure wasn't going to apologize for how he felt.

Kai pressed her lips together. John had said they needed to talk, and he wasn't wrong, she just hadn't expected it to be tonight. Now that they had started however, she needed to get it all out, no matter how difficult it was.

"There's also the matter of The Bond," she said, looking down at her hands.

John looked down at her sharply, a small frown forming between his eyes. His hand came up and touched his chest. "This?" He asked.

Kai nodded and swallowed. She wasn't sure she would be able to find her voice. "I haven't been entirely upfront or honest with information about it. The Bond is a intimate telepathic link between my people. It's not something Beckett would have known anything about it."

John flashed her a knowing smile. "I assumed."

When he didn't seem immediately angry Kai forced herself to continue. "I honestly thought it was a myth, something they claimed the primitive outland tribesman experienced when they found their life mates. Under the control of the grand council all attachment was forbidden. All matches were conducted in a lab. Even the idea of Bonding was outlawed..." Kai dragged off sucking in a breath. "I didn't even know it was real until I met you," she confessed.

John had known what he felt from time to time in his chest had something to do with Kai, he had just never realized the full extent of it. "So your people Bond when they get together with someone?" He asked.

Kai's lips pressed together into a line. She had told herself she wasn't going to lie to him and she wouldn't. Never again. "According to Mortii legend a Mortii will only Bond once in their life."

John's eyes widened in surprised, but inside he was secretly pleased as a possessive swell rose in his chest.

"I think," she continued and she took a deep breath to steady herself. She had to get this out or she would lose her nerve. "I think you should take the time to consider if your feelings are your own, or if...if what you think you feel is just the telepathic connection," kai finished, looking back down at her hands.

"You want me to take time and think about what I want, so I can be sure. But Kai," John said and he paused until she raised her storm colored eyes to meet his. "What do you want?"

Kai froze. She was fighting to contain her emotions but she was falling disastrously short. She knew how she felt about John, how she had always felt. She was terrified it was her own feelings being reflected in the Bond and she couldn't live with that question hanging over them.

"I-" she started to say and stopped as John took another step closer to her.

John tilted his head as he stared down at her, his hazel eyes incredibly intense. Kai's breath caught in her throat and a knowing smirk crossed John's face. He raised his hand slowly so she could move away if she wanted and gently tucked her damp hair behind her ear. "What do you want Kai?" He asked firmly.

Kai swallowed. "I-" she started to say again and had to take a deep breath to center her thoughts. She was not a youngling who couldn't think past her own hormones, but there had always been something different about John. "I think we should both take a week and decide what we want. If we go forward with this, it won't be easy," she said.

A boyish grin crossed John's face. "I've never been accused of doing things the easy way," he said and he winked at her as he turned to the door. She could say what she wanted, but it was clear how she felt. John would give her all the space she asked for, but he was fairly confident she wasn't going to run.

John hesitated in the door and turned back to face her. "One week," he agreed with a nod. "Sleep well."

The door slid closed behind him and Kai dropped down to sit on her bed, exhaling. She was exhausted, but the intensity of their interaction was likely to keep her up all night.

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Hope you enjoyed the update!!