Acknowledgements: Special thanks to Shelly for reading and giving feedback and very special thanks to Kathy for doing the beta thing on several chapters. All mistakes are mine, as they were just lending a hand (or an eye). Also, thanks to flowk and her story Outcomes and Consequences. Although this story is not related to that one in any way, her portrayal of John's father is what gave me the idea.

Note: I apologize ahead for mistakes in the medical or military aspects of this story. I did research the material, but didn't find enough to be very confident about some things. Let me know if I made any hideous or glaring errors so I can try to fix them.

Disclaimer: I don't own them, just borrow them from time to time.

Going Home – Chapter 1

John sighed and shifted around in the back of the taxi. He was exhausted and hurting from the flight. It had been a while since he'd flown in a commercial airplane and he'd forgotten how small and cramped the seats were. They seemed even more so when you were nursing a bruised body and a myriad of still sore and healing injuries. He'd wondered two minutes into the flight if he was making a big mistake.

But he was on the ground now and about ten minutes away from answering a question he was terrified of. His stomach churned and rolled itself up into a tight knot of bare nerves. The slumped position his tired body had been in set up an ache in his broken ribs, so he leaned to his right to alleviate some of the pressure.

"Are you all right, sir?" asked the cab driver, peering at him through the rearview mirror. The driver was black with short cropped hair and a mustache, and had fussed over him at the airport like he was a long lost cousin. John smiled at the genuine concern in the man's voice.

"I'm just a little sore. I'm fine as long as I don't move," he quipped.

The man chuckled, a deep and sincere laugh that made John relax a little. "Well, maybe when you get where you're going, you won't have to move around much."

John's smile faded as he remembered where he was headed. "Yeah . . . maybe." His gut clenched even tighter and he found his heart rate climbing. Looking down in his lap, he realized he had his fists clenched and the movement was pulling on his injured shoulder. He took a long, deep breath and let it out slowly through his mouth.

"So, are you're home on medical leave? Or are you done?"

John stared at the back of the man's head for a second before remembering he still had his uniform on. "Medical leave. They sent me home for a little rest and recovery period."

"You been in Iraq?"

John bit his lower lip a second, trying to figure out what to say. He teetered between just lying and saying yes or giving some vague answer. He really hated lying, especially to someone who had been so nice and seemed more concerned about him than the man he was going to see. "No . . . it's kind of an out-of-the-way place. I doubt you've ever heard of it."

He watched the man's reflection as his eyebrows shot up. "Is it classified?" he asked almost hopefully.

John grinned at the man's growing excitement. "Yeah, I could tell you, but then I'd have to kill you."

"Really?" the cab driver almost squeaked.

John chuckled. "No, I've just always wanted to say that. But it is supposed to be classified. Covert ops kind of stuff." Might as well make the guy's day.

"Wow, that's really cool. You know, I have a lot of respect for our people in the military. My brother served in Iraq last year. He came home safely, but he saw a lot of guys who were injured or killed. When he tells us about it . . ." He shuddered involuntarily. "Well, let's just say that it scares me more than any of these horror movies they have out now."

"I know what you mean," said John softly. He was glad the guy didn't know what was really out there. He jerked his head up when they turned into a driveway, fear gnawing its way into his soul in a way the Wraith or Kolya could never manage. He sat there for a moment after they stopped.

"Sir, we're here."

John swallowed and gave a curt nod. "Okay… thanks…" He opened the door and worked to get his legs out the door. His right thigh was beginning to throb with the off and on activity and movement of the day so that he found himself having to almost pick it up to swing it out of the car. His left arm was in a sling and bound pretty tightly to his body to protect his shoulder, so he tried to push himself up with his right hand. He looked up to find a hand extended to help. He hadn't even noticed the driver getting out of the car.

"Thanks," John said, allowing the man to help him up. It was that or waste ten minutes trying to do it himself. He hated this part of the recovery period. He felt well enough to want to do things for himself, but his body just wasn't ready to cooperate.

The driver watched John sway slightly. "I'll get your bag for you."

"Not yet," he said softly, staring at the cream colored house with dark trim, the yard mowed and edged with the precision he expected. "I'll let you know in a few minutes if I'm staying or not." He tried to ignore the sympathetic look he was getting from the cab driver. It was time to do this.

John stepped forward, his stiff body protesting loudly at the new movement so that he had to lean against the car for the first couple of steps. But he refused to stop. If he stopped at this point, he might never come back and he was to the point he needed an answer one way or the other. He needed to end the wondering if there was any way to recover what he'd lost so long ago.

He paused at the steps, knowing it would be difficult. Clenching his teeth, he carefully picked his way up the four concrete steps and limped to the front door. Giving himself a minute to catch his breath, he told himself he didn't care how this worked out, as long as it gave closure to the matter. Summoning his remaining strength, he knocked firmly on the door.

A horrible thought crossed his mind. What if he'd worked up his resolve to come here and he wasn't home. As a wisp of panic fluttered in his belly a moment, he heard footsteps approaching the door. He was here.

John was prepared, but he still flinched when the door opened. He stood looking at a man his height, but with graying hair and deeper lines around his eyes. He was thin, like John, but with slightly wider shoulders. Green eyes stared at him from a hardened face.

"Dad?" He wanted to kick himself for the way his voice faltered, sounding weak and timid. He had promised himself he'd be strong this one time.

And then the hardened expression melted away and the eyes softened, glimmering a bit as extra moisture collected on them. The man who had looked like a statue just a moment ago seemed to falter. "John?" he asked, his voice so low as to be barely audible.

John didn't know what to do. At worst, he'd expected to have the door slammed in his face. At best, he had hoped for a minute to apologize and explain what had happened while his father looked on in judgment. For a moment, he was a child again and his father was looking at him with the love only a parent can have. It threw off his whole rehearsed speech.

"Uh, dad, I . . . I wanted to apologize and . . ."

His dad stepped out and wrapped his arms around him, pulling him in so tight he felt like his healing ribs were breaking again. He could barely breathe and the muffled, choked voice from his shoulder didn't help.

"No, John . . . I'm the one who's sorry. God . . . I was afraid you were dead and I'd never get to tell you. I'm so sorry."

Slowly emerging from shock, John brought his right arm up around his dad and returned the hug, burying his face in his father's shoulder and squeezing his eyes tightly against the burning tears he was trying to hold back. His heart was racing, leaving him lightheaded and terrified he'd wake up to find this had just been a dream. He had no idea how long they stood there before they pulled back, each wiping their face as if they weren't wiping away tears.

His father looked over his shoulder at the waiting taxi. "Are you staying?" His voice was low and shaky, adding one more helping to John's plate of surprise.

"I . . . I wasn't sure if . . . I have some down time and I thought . . . " John mentally slapped himself for his complete lack of verbal skills at the moment. His brain was scrambled and didn't seem to be connected to his mouth at all, leaving him feeling like a fool. Until his dad broke out in a big grin.

"I'll take that as a yes. Go in and have a seat before you fall over and I'll get your luggage. You have luggage, right?"

John just nodded. "Yeah, one bag. And I haven't paid the guy yet. I was waiting to see . . . "

A sad look flashed across his father's face for a second as the man nodded. "I understand. Go sit down son, you look done in."

John was suddenly afraid. This was way too good to be true. He had a mental image of letting the cabbie go and going in, only to have his father return and verbally attack him once again. He swallowed hard, uncertainty filling him as time seemed to drag by and his dad watched him.

"John . . . I've made a lot of mistakes. Please, give me a chance to make it up to you."

The sincerity in his father's voice combined with the love for his dad he remembered from his younger years to override his fear. "Okay . . . guess I'm staying for a while."

His dad grinned and nodded, bobbing his head up and down in excitement. "Good. We have a lot of catching up to do. Now go sit down while I get your bag." Without waiting, the man hurried down the steps and out to the waiting cab driver, who met him halfway up the path, John's bag in hand.

"He's staying?" he asked, jutting his chin out and narrowing his eyes at John's father.

John's father regarded the man for a moment before answering. "Oh yes, my son will be staying, how much do I owe you?"

The cab driver shook his head. "You don't owe me nothin', I've got a brother who served…" As he turned back to the cab he caught sight of John still leaning on the door frame. John nodded his thanks. The driver could see the relief on the younger man's face and flashed him a quick smile and mock salute before turning away.

The living room was just as he remembered it, except there was a new sectional taking up most of the left side of the room. It was dark brown with an easy chair at each end and one in the middle. Nice. He eased himself down into the nearest one and let himself relax back into the cushions. The relief was almost painful. He knew he had been tired from the trip, but he hadn't fully realized how tired. Looking across the room, he noticed his dad had gotten a new TV as well. A nice big screen TV on a matching stand sat directly in front of him.

The door opened and his dad came in carrying his bag. "I'll just set this in your old room. I have it set up as a guest bedroom now, you'll be comfortable in there." He disappeared down the hall, returning a few seconds later. "Would you like something to drink? A beer maybe? Or is it too early for that?"

John smiled and shook his head. "No, I can't. I'm still on medication and under strict orders to stay out of the alcohol. Which kind of ruins the fun of being back home and truly off duty. I haven't had a beer in . . . I don't even know when."

"I have tea or Coke or I could make us some coffee."

John thought his dad looked like he was ready to bust at the seams to get something for him and, truth be told, he was thirsty. "How about a Coke?" That actually sounded good since they didn't get them very often, even with the runs from the Daedalus.

"Great." The older man rubbed his hands together and made a bee-line for the kitchen, his relief at being able to do something painfully obvious.

John leaned his head back against the cushions and closed his eyes. His head, shoulder, and leg throbbed incessantly, leading him to realize it was almost time for another round of pain meds. He wanted so badly to lie down with his drugs and let the pain fade away for a while, but he needed to face his father first.

"John?"

The voice was so soft, it took a moment for him to react to it. He opened his eyes and looked into the worried face of his father. For a moment, he was six and had just fallen out of the tree in their back yard. Blinking a few times, he noticed the Coke in his dad's hand.

"Oh, thanks." He reached out and took the cold can. It had already been opened, so he took a few swigs, relishing the cold burn of the carbonated drink sliding down his throat. He set the can down on the coaster sitting on the side table and looked at his dad, who had taken a seat in the middle easy chair. That left them close enough to have a comfortable conversation, while leaving enough distance for each to have a safety zone around them.

"Dad, I wanted to explain, to tell you why I did what I did. I know I've sometimes done some crazy things on a whim, but this was different. I wasn't trying to be a hot shot. I had a reason for going after Holland." John had practiced his speech about a million times over the years. He was ready to make his defense. He was shocked that he didn't get the chance.

"I know why you did what you did." Joe Sheppard bowed his head and shook it a couple of times before getting up to pace back and forth. "I should have known the minute I read that report, but I was too busy being a bull-headed fool. It took a friend pointing it out to me a year ago for me to finally see what was in front of me the whole time." He stopped and stood before John, looking down at his son. "You were doing what I taught you since you were old enough to walk. You weren't leaving anyone behind. And if I'd had any sense, I'd have been proud of you instead of tearing you a new one."

John's heart was beating so fast he wondered if it might explode. His dad really did understand. After all these years, he understood. He felt the moisture beginning to build in his eyes again and he rubbed his face in order to get rid of it. The exhaustion and the flood of emotions were making him dizzy. When he opened his eyes, his father was sitting beside him.

"John . . . I'm sorry for the years of pain I've caused you. And I know that started long before the incident in Afghanistan. I just hope you can forgive me and we can start all over, maybe make a new relationship. I'm pretty sure I've ruined the old one."

John shook his head, an act he quickly decided wasn't one he planned on repeating. "No, dad, it isn't all your fault. I spent some time pushing your buttons and making it worse, I know that now. But there's still a lot of good years in there that I don't want to leave behind. We just need to work on making it right again."

Joe's face relaxed and John realized that his dad had been as terrified of this moment as he had. The tension began to fade away and his stomach began to unclench from its tight knot. He was suddenly very glad he had decided to risk coming. He found himself surprised at how good it felt to have a father again.

Joe stood up and looked toward the kitchen. "Are you hungry? What is it, almost three?"

"No, I ate on the plane, sort of."

Joe made a face. "I doubt that was very good. I'll take us out to dinner tonight as a celebration. How does steak and the biggest baked potato in town sound?"

John grinned. "Now you're talking my language."

Joe studied his son a few moments. "You look tired. Do you want to lie down a while before we go?"

"Yeah, that's probably a good idea. Doc says I'm coming along pretty good, but I still get tired too easily." He didn't tell his father that he was hurting so bad it was almost bringing tears to his eyes, but he suspected his father knew when he appeared at John's side, helping him out of the chair. Leaning heavily on his father as a wave of dizziness passed, he mentally chastised himself for being so weak.

"It takes a while, John. Be patient."

John looked at his father as his head cleared. "I see you still read minds."

Joe grinned. "That's right, so don't be trying to hide anything. Let's get you to bed."

oOo

Joe Sheppard sat down in his chair, staring blankly across the room. He was still trembling slightly at the rush of seeing John. Part of him had been convinced that John was dead, killed in some special ops suicide mission. He'd tried every contact he'd ever had over the past year, trying to find out where his son was. The most information he ever got was, "It's classified". He'd spent a lot of sleepless nights, mourning his son and the fact that his last words to him had been harsh and foolish.

But now he was sleeping in his old room. Joe had helped him to the bed and gotten him a glass of water so he could take his pills. The boy hadn't said anything, but he could tell he was hurting pretty badly. He hoped in time John would tell him what had happened to him. John had a new scar, still red and angry, across the right side of his forehead and arching down to his temple where stitches had recently been removed. His shoulder and ribs were obviously giving him trouble and he was limping from a leg injury. There was no record for where he had been for almost three years. The boy had to be involved in something big.

Big and dangerous, from the looks of it. John had always managed to find trouble. When he thought about it, it was usually due to one of two things. He always looked out for his friends and the underdog, taking up for people even when odds were against him. And he had sense of adventure that led him to try almost anything. Joe smiled to himself when he remembered his wife once telling him the people at the hospital were going to think they were abusing John because of the number of trips to the emergency room they had made. She hadn't been amused when he'd pointed out that they would probably get transferred soon and then they could start all over again.

He found himself going back to John's room and peeking in the door, making sure his son was really there. John mumbled something in his sleep, moaning softly as he shifted. Joe decided he looked cold, so he crept over to the closet and pulled out a blanket as quietly as he could. Unfolding it, he carefully draped it over his son, who shifted restlessly, his brow furrowed, even in sleep. John mumbled a few words that sounded disturbingly like a plea to stop, and then went quiet. As Joe slipped out of the room, he couldn't help but worry about what his son had gotten himself into now.

oOo

John came awake with a start, his breaths coming quickly and his hairline damp with sweat. Easing back against the pillow, he took a few minutes to calm his pounding heart and slow his breathing down. He looked up as the cracked door opened a bit more and his father's head appeared.

"John, you okay son?" the worry in his dad's face and voice plainly evident.

"Yeah, I'm good. Just getting up."

His father nodded, but he was studying him in a way that suggested he didn't quite believe him. "Need any help?"

"Nah, I can handle it. What time is it?"

Joe looked at his watch a moment. "Uh, almost six fifteen."

John sighed. He hadn't meant to sleep that long. "Okay, let me wash my face and change clothes and we can go."

"What you have on is fine . . . unless you want to change."

John realized his father wanted him to wear the uniform. He was proud of him and wanted to show him off, something John had never thought would happen in a million years. He grinned, feeling like his pounding heart had expanded to take up his whole chest. "No, this is fine. I'll be out in a few minutes."

Joe broke out into a big grin. "Let me know if you need anything."

John used his good arm to push himself up into a sitting position to prove to them both he could take care of himself. "Okay." He watched his father pull the door closed except for a small crack and head back down the hall. Grunting at the pain the movement caused, he managed to twist around and get off the bed. He smiled as he hobbled toward the bathroom, stretching out his stiff muscles. His father was actually proud of him.

As John washed his face and got cleaned up, he wished he could tell his father what he'd been doing the last three years. He wanted to share meeting Teyla and Ronon, discovering a whole new galaxy, flying puddle jumpers, and his weird connection to Atlantis. He wondered if his dad had the ATA gene or if he'd gotten it from his mother. Or maybe both. It saddened him to realize he could never know the answer. He dried his face and left the bathroom. Reaching out to pick up his cell phone from the bedside table, he stared at it for several seconds. A smile slowly broke out over his face.

He quickly dialed the phone and waited. Several seconds later, he was connected to General Landry at the SGC. "General Landry, sir, this is Colonel Sheppard." He paused to listen. "Yes, sir, I made it fine. Sir, I have a very special request to make."

TBC

Sorry I haven't been around much lately – just really busy. I hope to post every other day (hope being the operative word here).