NOTE: Thank you so much for the reviews. I'm sorry I don't have enough internet time to answer them all. Landry is kind of jerk in this one and I'm sorry if that is too out of character. He kind of rubbed me wrong in Part one and I guess I just built on what looked to me like a total disregard of the Atlantis team's knowledge and abilities. He would never have treated SG1 like that. Anyway, sorry if I went overboard.

The Return Part 2: Favorite Son - Chapter 3

John was pretty sure he had memorized every minute detail of the infirmary ceiling. Actually, he'd done that long ago, but he'd spent the last several hours rediscovering everything. It was late and the infirmary was dark, but John couldn't sleep. The hum of Atlantis that had been so welcoming before now seemed to thrum just beneath his skin like an electric current. He'd always felt the connection before, but it usually wasn't so insistent. It reminded him of some long lost relative that was hugging him too tightly and just wouldn't let go. He relished her presence, her touch, but it filled him with a nervous energy that would not allow him to relax.

John longed to get up and walk around, to go to the nearest balcony and spend some time watching the moonlight reflect off the ocean waves. He lifted his head a few inches to see his guard was still standing by the door. He could probably take the guy, but then he'd have to deal with Carson and Elizabeth, so he decided it just wasn't worth it. Sighing, he rolled over for the tenth time that night, trying to untangle the blanket and sheet from around his legs. In the process, he pulled one of the electrode pads off his temple, sending an alarm blaring.

"Well, crap!" He sat up and started to turn around and find a way to turn the machine off, but froze when he heard a gun cock.

"Freeze, colonel!"

John did what he was told, having no desire to be filled full of holes just because he was having trouble sleeping. He raised his hands slowly and turned to face his guard and the gun pointed directly at his chest.

"Sergeant, let's not overreact here. I just pulled one of those lead thingies loose." John was relieved to see Carson and Emira coming out of Carson's office. Or rather Emira's office. He really hated this.

"Put that gun away, it's just the monitor alarm. Colonel Sheppard isn't going anywhere," said Carson sharply as Emira moved past him and turned the alarm off.

"I was trying to turn over and I guess I pulled too hard," explained John. "Sorry."

The soldier finally let his gun drop and nodded, moving carefully back to his position by the door. He never took his eyes off the prisoner he was guarding.

Emira reattached the pad to John's temple and turned the machine back on. "There you go, colonel. All fixed."

John grimaced. "Gee, thanks. I'd rather you just got rid of it."

Carson shook his head. "Not yet, colonel, we're still getting some odd readings in your EEG. I got rid of the other monitors for you, but this one stays a wee bit longer." Carson fixed John's pillows and straightened his covers as he spoke.

"Thanks mom," John said dryly.

Carson smiled and gave a short nod. "You're welcome, son."

Emira watched John's EEG readings for a few minutes before turning back to him. "You can't sleep, can you?"

John sighed and shook his head. "No, not even close. I'd love to get up and stretch my legs, but I'd probably get shot."

"I could give you something to relax you," offered Carson.

"No, no drugs. Besides, I'm pretty sure it wouldn't help. It's . . . " He really hated saying it, always afraid people would think he was nuts or a freak.

"It's Atlantis, isn't it?" asked Emira.

John hesitated a moment, until Carson nodded at him. "Yeah, it's Atlantis. With everything that's happened, she's a bit . . . overenthusiastic right now."

"What does it feel like?" asked the Ancient doctor, leaning a bit closer.

John took a deep breath, hating these kinds of questions. He tried to collect his thoughts into something that sounded reasonably sane. "It's hard to describe, and it's not always exactly the same. Right now I kind of feel like I have one finger in a light socket, but it usually isn't that strong. Unless I'm in the chair and that's . . . that's another world entirely. I can feel her, almost like she's standing next to me. I can tell when new systems are brought on line if they're very big or I'm not doing anything at the time. For example, I think they switched over the power grids about an hour ago. And I'm more in tune with her now than before we got sent back to Earth. It's like . . . she missed me so she's holding on tighter." John rubbed his hand over his face. "Look, I know how crazy that sounds."

Emira shook her head. "No, it's not crazy at all. Carson and I have been studying your EEG. We don't have your previous readings with us right now, but Carson is pretty sure he remembers them enough for us to determine some differences between before you left and now."

John frowned, not entirely sure he wanted to know any more. "Like what kind of differences?"

Carson smiled and patted John's arm, being his usual reassuring self. "Well, lad, you're EEG reading have always been a tad off the rest of us, at least since coming to Atlantis. By talking with Emira tonight and looking at your current readings, I know why. Ancient EEGs have a slightly different pattern than humans and apparently yours are somewhere between the two. Now we aren't talking major changes, so you don't need to worry. But we've noticed some anomalous patterns that appear ever so often that don't match human or Ancient. We noticed one about an hour ago, so I'm assuming those show up when you are having a more direct contact with the city."

"This is really fascinating," said Emira. "I'm hoping Helia works it out so you can stay. Carson and I have already talked about how much we have to learn about how this connection works and why it is so strong in you. Carson said he has extensive DNA studies for you when we are able to get your records from Earth. We want to go back to various test results from your days before Atlantis and compare them to ones done over the years you were here. This is all very exciting."

John stared at the two for several seconds, the feeling of unease growing in him. "So, basically you plan on using me as a lab rat."

The wide smiles on the faces of the two doctors slowly disappeared as they exchanged a look. Carson frowned as he looked down at John. "No, not at all. We just want to run a few tests and, uh, well there is just so much we don't understand and we need to , uh . . . " He sighed and rubbed his forehead for a second. "I guess you're right. We were planning on turning you into a bloody lab rat."

John gave a low, rough chuckle. "It's okay, Carson. I understand that scientific curiosity thing better after spending the last few years working with McKay. And I understand that, for security reasons if nothing else, we really should learn more about the connection and how it works. I just want . . . I want you to remember that your lab rat is human. That sometimes I need a break from it. That sometimes I just need to feel . . . normal for a while." John paused and looked uncomfortable for a moment. "Mostly, I just want to be able to say stop sometimes and have someone listen," he added quietly.

Carson and Emira looked at one another sheepishly and then back to John. "You're right, of course," said Emira. "I guess we just got all caught up in the mystery."

Carson nodded. "Aye, that we did. If we end up staying, I guarantee that we'll ask to do these informative tests, not order and that you will have the option of saying no if you want."

John nodded. "That's all I ask."

Emira smiled. "And in the spirit of listening to our patient, I think we could suspend the EEG monitoring for the night to make it more comfortable for you."

Nodding, Carson glanced around the room before looking back to John. "Aye, and I think we could let you get up for a few minutes to walk around the room a time or two. It's not the balcony, but you could stretch your legs."

John grinned. "Really? What about the IV?"

Carson laughed as he shook his head. "Nice try, colonel, but you'll just have to roll the IV pole around with you. That stays for now."

John was already sitting up and pulling the blankets back as Emira tried to get him to hold still for her to remove the pads on his temples. "First stop is the little pilot's room," John said.

Emira paused and looked at him strangely. "The what?"

Carson nodded toward the bathroom with his head and Emira smiled. "Oh."

John noted the guard tensing and turning toward them, his gun having come partway up. "You better tell the guard what we're doing or we'll all be shot. It'd be just my luck to get killed by our own people for trying to use the bathroom after surviving that crazy mission against the Replicators." He was a little miffed when Carson laughed.

oOo

Carson watched Emira as she studied Sheppard's charts, squinting slightly in concentration. He was pretty sure that her eyes were the brightest green of any he'd ever seen. He smiled, thinking about her easy going manner and light sense of humor. They hadn't been working together long and yet he felt like he'd known her half his life.

"Carson, are you listening to me or daydreaming?"

Carson blinked and focused on what Emira was saying. "What? I'm sorry, I must have let my mind wander," he said sheepishly. Undoubtedly the way to not impress a lady was to totally ignore what she was saying.

Emira just smiled coyly as she looked Carson right in the eyes. "I might be insulted if we hadn't been up most of the night with the Colonel and studying his test results. I know you're tired, though, so I'll forgive you for not paying close attention."

Carson chuckled, relieved that she didn't have her feelings hurt by his inattention. "Right, sorry. I was just . . . " He trailed off as someone entered her office and they both looked toward the door. Carson recognized the woman immediately and stood up, surprise filling his expression.

"Dr. Lam . . . what are you doing here?"

Her expression and tone of voice were flat and completely devoid of emotion. "General Landry has sent me to evaluate Colonel Sheppard's condition to determine if he's fit to be returned to Earth. I'd appreciate it if you would show me to him now."

Carson was speechless, caught completely off guard by the sudden appearance of Landry's daughter. He'd thought they might have a little more time. Realizing what she would find, anger began to fill him. "So, General Landry can't even wait a few days to ruin a man's life for saving a city, almost a hundred lives, and possibly a galaxy. I guess the taste for blood is a strong one."

Lam's face remained emotionless. "I'm just here to do my job, not to make judgment calls on motives. If you'll show me the Colonel, I'll examine him."

"Fine," Carson said angrily, leading the way from the office and making a show of steering around Dr. Lam. His anger increased when he left the office to find four marines waiting outside, presumably to escort the Colonel to his prison cell on Earth. Carson felt his stomach tighten as he tried to think of a way out of the situation.

Sheppard was still dozing when they approached. Around mid-day, he'd said Atlantis was finally beginning to calm back down and the buzzing in his head was laying back enough he could get some rest. Exhausted, he'd slept or dozed most of the afternoon. Almost as if he sensed what was coming, his eyes snapped open at Dr. Lam's approach.

"Colonel Sheppard, good, you're awake. I need to examine you to determine if you are well enough for possible extradition back to Earth."

John looked up at Dr. Lam and then at the four marines standing at the foot of his bed. He sighed, his expression dropping. "Why don't we cut the crap. Landry wants me back promptly for my crucifixion so you're going to find me ready to go. Just yank the IV and let's go. We both know that'll be the end result, anyway."

"I haven't examined you yet, so I don't know what your condition is," said Lam.

John's eyes smoldered with anger. "Yeah, whatever. Well, then do your little dog and pony show of taking a few vital signs so you can declare me ready to travel. Let's just get this over with."

The lights in the infirmary suddenly flickered several times and then went off.

"What's going on?" asked Lam, fear finally putting some emotion into her voice.

"That would be Atlantis," said Emira. "I suspect she's registering her displeasure with your little mission here."

Low level emergency lighting slowly came up, only slightly brightening the dark infirmary. Lam and the four marines were all looking around nervously as if they expected to be attacked.

"You don't seriously expect me to believe a city cares whether we take the Colonel or not. I'm not a complete idiot," said Lam angrily.

John sat up and pulled his IV out, throwing his legs over the side of the bed. Four guns came up and were immediately leveled at him. "Oh, stand down. You want me to go with you don't you. Let's just do this and get it over with. Can I at least put on clothes or do I have to be marched through the city in scrubs?"

Dr. Lam was extremely exasperated by now, having fully lost control of the situation. "I need to examine you first, so please lie back down."

"Colonel, do as she says and lie down. You might as well not make it easy on her," said Carson. Walking over to John, he grabbed band-aide from a nearby cart, wiped the blood from the back of the colonel's hand, and bandaged the wound from the IV.

John pulled his hand back as soon as Carson finished. "No. Look, I just want to leave. If I don't do this now, I won't be able to leave her again. And you're just making it harder on Atlantis. Get my clothes."

Lam was furious. "Fine, we'll go without an exam. And if you fall on your face, it's your fault, not mine. Get his clothes."

One of the nurses brought John's clothes over and handed them to Carson, who then handed them to John. John took them and looked around the room. "I'll see if I can get her to turn the lights back on for you," he said to Carson. A few seconds later the lights flickered and came back on. "I reminded her it wasn't your fault and told her it wouldn't change anything."

Lam glanced nervously around the room, as did the marines. "You . . . you did that?"

John looked at her, his expression hard. "Yeah, she likes me that way. That's something General Landry will never understand. Now, can I dress in private, or did you want a show?"

Lam nodded. "We'll just be waiting out here." She stepped to one side as Carson pulled the privacy curtain.

"I'm sorry, lad. I didn't think they'd come for you so soon," said Carson sadly.

John nodded. "I know. It's okay, Carson, you did what you could and I appreciate that. Tell them to take good care of my girl for me."

Carson nodded. "I will," he said as he moved to the outside of the curtain. He wasn't sure who would be more lost, Sheppard or Atlantis.

oOo

"General Landry, with all due respect, sir, this is very unfair. John . . . Colonel Sheppard is still recovering in the infirmary. The least you could do is wait until he's released. Surely saving this city is worth something." Elizabeth hated feeling like she was begging, but if that was what it took, then she was perfectly willing to do it.

"Look, Dr. Weir, I know since you aren't military, you don't understand the significance of what Colonel Sheppard did. He defied a direct order that was given three times. I can't let insubordination like that go unpunished. I told him I'd make sure his military career was over with if he insisted on going through with his little stunt and he did it anyway. I plan on keeping my word."

Elizabeth gaped at the general on the viewscreen. "That's what this is about, keeping your word to destroy a man because he dared to defy you? Look, General, I realize this seems to you like Colonel Sheppard just ran off half-cocked with no thought to your orders. I can assure you that is far from the truth. It was obvious to all of us with him that he was very concerned about going against your orders, but you have to realize that you were making an uninformed decision. It's not your fault, but you don't know anything about Atlantis or how it works. John knows this place like the back of his hand and he interacts with this city like no one else can. He was the more informed of the two of you and he knew his plan could work. He also knew that there was no way to make you understand that in the limited time available. John did what he did to save a city and a lot of people and he did it knowing that he had a good chance of success."

"General," said Helia, standing beside Elizabeth. "I would once again like to request that Colonel Sheppard and his people be allowed to stay on Atlantis. I realize now that we were a bit hasty in sending everyone back to Earth. We would be very grateful for their help, and perhaps, in return, we could offer our help on certain things. I believe our two people might eventually become allies against a common enemy."

Landry seemed to hesitate a moment, giving Elizabeth cause to hope, when the sounds of people approaching drew the attention of everyone there. She felt like her stomach dropped to her feet at the sight that greeted her. Four marines entered the gate room, surrounding a very pale looking John Sheppard. His hands were bound in front of him, the look of humiliation and defeat on his face enough to make her feel physically sick. He made eye contact with her and nodded, the typical grin nowhere to be found. Elizabeth turned back to screen.

"General, please, don't do this. John is a good man and good soldier. He's given so much of himself the last two years. I just don't understand how you can ignore the sacrifices he's made, the pain he's endured, or the lives that he's saved. How can it be fair to undo all of that because he happened to know more about a conflict situation than you did? Don't make this a personal vendetta."

"Colonel Sheppard will be escorted back to Earth immediately to stand trial. If what you say is true and all of his other accomplishments outweigh this act of defiance, then he'll be acquitted. I also expect you and Dr. Beckett and Dr. McKay to return as well, although since you are civilians, I don't suppose you'll have to stand trial. Consider yourselves lucky."

The lights flickered several times, causing everyone to look around. Elizabeth glanced down at John and he looked up at her and shrugged his shoulders. She couldn't help thinking she'd never seen him look so lost.

"What's going on over there?" asked Landry sharply.

Elizabeth turned back to the screen. "Atlantis doesn't want him to go."

Landry just grunted and shook his head in disbelief. "Putting on your little light show changes nothing. Sheppard will be returned to Earth immediately."

Helia frowned at the general. "Am I to understand that your government does not wish to continue negotiations with my people?"

General Landry shook his head. "No, of course not. The President has expressed a very big interest in continuing our talks. Since you are now willing to have some of our people in Atlantis, I'm sure I could provide equally qualified representatives of our world to come there immediately."

Helia smiled up at the image of the general. "No, you misunderstood my offer. The offer was for Colonel Sheppard and his team. If they are allowed to stay, I will consider letting others come as well at a later date. At this time, the offer is only extended to the Colonel and his people. Now, do you want to work with us or not?"

Elizabeth turned to hide her smile, knowing it wouldn't be seen by Landry as anything good. She looked down at John, his face so full of despair that it almost hurt to look at him. She noticed the marines guarding him looked uncomfortable, as did Dr. Lam standing behind them. Smiling, she winked at him in an effort to pass on her hope and turned back to face Landry. Even though his projected image was a bit fuzzy, she could almost detect the flush of anger in his face.

"General Landry, what will it be?" asked Helia, pressing the man for an answer while she had him pinned down.

Landry finally sighed and nodded. "All right, he can stay for now while I consult with the President. I'll relay your offer to him. Have my people return to the SGC for now and I'll contact you later with our decision. Landry out," he snapped.

Elizabeth suddenly felt so weak and shaky that she wasn't sure she wouldn't collapse on the spot. She looked around at Helia as she gripped the back of the chair in front of her. "Thank you," she managed to whisper.

Helia smiled and nodded. "I meant what I said. I do believe we can learn a lot from each other."

Elizabeth nodded in agreement. "As do I." She turned and took a few steps toward the rail, looking down at the marines waiting below. Savill was with them and apparently conveying General Landry's orders because they were releasing John from the plastic strips binding his wrists together. She thought she heard one of the men apologize to him and then they walked through the still open stargate back to Earth, with Dr. Lam right behind them. As soon as they were gone, the gate was shut down. She headed down the steps, watching John as he stood facing the gate, almost like he was in a trance.

"John?" she called as she rushed to his side. He slowly lowered his gaze to meet hers. "I thought this was it, that I was leaving and never coming back. I don't know how you did it."

Elizabeth grinned as she gripped his hand. "Helia is the one you should be thanking. She told General Landry if you didn't get to stay, then there would be no talks with people from Earth. That got his attention. He knew the President would roast him if he gave up an opportunity to work with Ancients because of his pride."

"I'll never be able to thank you enough," he said to Helia. "Or repay you. But I'll do anything I can to help you, just ask."

Helia nodded as she smiled knowingly. "I'll remember you said that, Colonel. But make no mistake about it, after what you did for us, there was no way you were going through that gate if you didn't want to. If your General Landry had not accepted my terms, we would have simply sent his people home without you. We owe you a debt that I fully intend to honor in every way I can. You are welcome here for as long as you want to stay."

John smiled weakly as he looked around the gateroom, almost like he didn't believe he was still there. "Well, thank you. I think you just evened us up and I'm grateful. I don't really have anything or anyone on Earth I need to return to. This is my home now, and it has been for a while." He looked down at Elizabeth and nodded to her. "This is our home now." He swayed a little as a wave of dizziness hit him.

Elizabeth quickly slid her arm around John's waist, pulling him close in an attempt to get him to lean on her. "Come on, let's get you back to the infirmary before you fall on your face."

"What if I don't want to go back to the infirmary?" asked John.

Elizabeth looked up at him, her expression dead serious. "Where else are you going to go? You don't have a room any more."

John looked at her for a few seconds. "Dang . . . I don't. Guess we'd better go back to the infirmary then."

Elizabeth looked at Helia. "I'll get him back to bed."

Helia smiled at them both. "I need to stay here, but I'll come by later. Welcome back to Atlantis."

John nodded. "Thanks. Okay, let's go." As they headed across the gateroom, John suddenly laughed. "Man, is Beckett gonna be surprised."

Elizabeth gripped John a little tighter as Rodney rushed into the gateroom, almost knocking them down. He was red faced and puffing, his expression one of full blown panic.

"Did I miss him . . . oh . . . you're still here." He looked around wildly before settling his attention back on the two former city leaders. "What's going on? Carson . . . called me and told me . . . they were taking John back to Earth in restraints."

John sighed, but grinned. "Better slow down and catch your breath before you give yourself a heart attack, Rodney. I get to stay."

Rodney's breaths were finally beginning to slow enough to make talking easier. "Really?"

Elizabeth nodded. "Helia told General Landry that if John was forced to go back, they would cut off all ties to Earth. He didn't have much choice after that."

Rodney looked impressed. "Nice move. If Landry pisses off the Ancients, the President will have him for breakfast. I like it." Rodney looked at the way Elizabeth was supporting John. "Maybe you should get him back to the infirmary."

Elizabeth raised one eyebrow. "That's what I was trying to do."

Rodney sidestepped so they could pass and held out his arm dramatically as if ushering them along. "Well by all means, please continue, because I'm not carrying him if he passes out."

"That's good, because I don't want you carrying me."

Rodney looked slightly offended and then fell into step behind them. "Hey, do we all get to stay or just gene boy?"

"McKay, stop calling me that," John snapped.

Rodney grinned silently for several steps. "Hey, if the gene fits . . ."

"Enough," said Elizabeth tiredly. "If you two don't stop, I'm sending you both to bed without supper. I swear, you two would drive Job insane."

Several minutes of silence followed as they walked down the corridor. "Uh, you never answered my question. Do we all get to stay?" asked Rodney in his most penitent tone of voice.

"Everyone but you," quipped John.

"Just arrest me now, because I'm killing both of you at the first opportunity."

TBC

The bad news is that I'll be out of town (yet more science fair) Friday and Saturday, so it will be Saturday night or possibly Sunday before I can post another chapter. Sorry about that. Happy egg hunting.