Fatherhood. It sounded like a simple enough concept in his head. But it had been, by far, the hardest task Rodney McKay had ever taken on in his life.

Fatherhood was unpredictable. No matter how many times he sat down at his desk and tried to map it's subtle intricacies or grasp all of its interlocking and meandering parts, it remained a mystery.

Fatherhood had no strict set of rules, no structure - despite what the plethora of books he'd read on the subject had tried to tell him. As a scientist, his world had been ordered by facts and principles, but there was no principle that ever could have prepared him for what it would feel like accepting that sleeping child into his arms. No equation to dictate how he should feel as he begged Diane not to tell anyone what he was about to do or judge him for the decisions he'd made.

Sometimes late at night when some problem with his wormhole research wouldn't let him sleep, Rodney McKay would think back on that moment and wonder if he had done the right thing.

Maybe he should have pushed harder to get the trapped Athosians back to Pegasus. Or at least got word to Kanaan somehow that his son was safe. That would have entailed telling the SGC all about Torren John (or TJ as they'd taken to calling him). If they reacted the way normal human beings should react to a helpless infant and not see him as an alien from another galaxy, then maybe they could have found a more suitable home for the kid.

Rodney had never been what anyone would call "father material" but there was really only one conclusion he'd be able to come to during those long hours of the night when sleep was elusive. One simple and irrefutable fact: Torren John was his .

It wasn't how it was supposed to work out. It wasn't perhaps what the universe had intended for any of them really, but Rodney McKay had fallen in love with that little boy and had done the best he could in raising him.

Back on Atlantis, he would have been the first to admit that he didn't have the slightest idea what to do with kids. His interactions with the children on the worlds they visited could attest to that. But the day he'd left that tiny apartment he shared with Diane as a scientist and returned to it later that night as a father, all that changed. Suddenly the Gods of Science were being replaced with diapers and baby food. Subspace research was pushed aside to make room for the worries that plagued him about the SGC finding out about what he had done and trying to take his son away from him. Diane had been his rock through all of it; the glue that had held him together at times. Between the two of them, they'd managed to raise one pretty damn impressive young man. TJ was smart, strong, top of his class and Rodney McKay had never been more proud of anyone else in his life.

Details of the past 18 years were sitting on the tip of Rodney's tongue just waiting to be revealed, but as he turned once again to face the old friend that sat perched on the stool beside him, Rodney found he just couldn't do it.

Ever since that day a week ago when he'd ambushed Sheppard in his little cabin in the woods, all Rodney had brought the man was more misery. It had started with that disaster of a conversation where he'd practically blamed John for the deaths of Cameron Mitchell and Samantha Carter and had ended just now with Rodney dropping the bombshell that he'd raised their dead friend's son. A truth made even heavier by the fact that the Athosian had wanted that particular job to go to Sheppard. Rodney was getting himself into the middle of things he knew nothing about and instead of aiding everyone in putting John Sheppard back together, he was only helping pull him further apart.

Not only did John have the weight of the past to contend with, but now the uncertainty of the future. A future muddied by the impossible expectations of the present. If Rodney thought about it, he was amazed the aging soldier was sitting on the stool beside him at all. That he hadn't just thrown in the towel ages ago and said to hell with it. The fact that he hadn't was a testament to the man John Sheppard was, he figured.

Rodney had thought a lot about his old friend over the years. He could only imagine what kind of a life Sheppard had led. The thought of always being on the run, of never being allowed to stop and to settle was not an idea that Rodney McKay could easily wrap his head around now. His own life had been far from predictable but he'd fought hard to get it to a place where everything didn't feel like it was about to come crashing down around him. John Sheppard had never been afforded that luxury. As far as Rodney knew, anyway. He hadn't really gotten up the courage to ask Sheppard difficult questions like that just yet, and maybe he never would. Rodney had never been good with things like that and he knew the preconceived notions people usually developed about him because of it. Rodney had softened a little over the years because of TJ, but he still really didn't know how to help the man sitting on the stool beside him.

John Sheppard was hurting, and it wasn't just from the bruises still mottling his face in sickly greens and yellows. It wasn't a scrape on the knee after a tumble over the handlebars that just required a little TLC. This was a serious, crack down the middle of the soul kind of hurt that Rodney McKay had no idea how to repair.

Like fatherhood, there was no basic scientific principle for him to fall back on and he only seemed to make matters worse when he tried to fix things. He'd just never been any good at offering comfort - of finding the right words to ease someone's pain - and it was like the universe had set him in the middle of a cornfield in Iowa, told him it was his job to help John, but had overlooked one small, yet important fact: he was no Kevin Costner. He'd managed a few 'ah-ha' moments over the past several days, but it wasn't anywhere near Carson's suggestion that he try to get John to open up and talk about things again. Or what was going on in his head now, for that matter.

The truth was, Rodney was dying to talk to his friend about what had happened all those years ago. He had a feeling his version of events and John's were very different.

Rodney knew, for instance, that everyone involved in the mission that day had their own 'what if' moments, and that he wasn't the only one who looked back on the past and wished he'd done something differently. For Rodney, it was the moment he'd realized Woolsey had cut off all communication with John in the control chair room and Rodney hadn't been able to reach him.

In his 'what if' moment, Rodney had torn his eyes away from the Star Drive outputs and demanded an explanation from Woolsey, eventually beating a confession out of the man with his fists before informing a thankful John Sheppard of what he'd just nearly done and sitting down to come up with some better plan to save their people. Rodney was a bit of a hero in that scenario, but he figured it was just his brain's way of trying to make sense of the madness that day.

In reality, Rodney had been so absorbed with making sure Atlantis didn't get blown out of the sky by her own overheating systems, that he'd barely even registered the fact that John wasn't communicating with any of them anymore. The loss of Teyla and Ronon... it had hit everyone hard, but John most of all, and he'd needed all his attention focused on flying.

Rodney hadn't really gotten any indication that anything was amiss at first. Besides, well, the hostile fleet of alien space vampires attacking Earth. It wasn't until an unscheduled off-world activation had been announced and Rodney heard the tech behind him tell Woolsey that it was Carson Beckett. That was the first moment Rodney felt like something was off because Carson was supposed to be down on Earth manning the weapons platform at Area 51.

But it was the moment of silence that followed the tech's request to lower the protective shield and admit Carson that really sent Rodney's heart into overdrive. That barest hint of hesitation from Woolsey that let Rodney know something was very, very wrong. For one brief, horrible moment, Richard Woolsey had actually contemplated letting Carson Beckett impact the protective shield surrounding their gate, then let him reach Atlantis. He'd given the order soon after, but Rodney was already overriding the controls and lowering the shield himself.

He would never forget the look in Carson's eyes as he rematerialized on the other side of the event horizon. Rodney had taken the steps down two at a time, nearly falling down the last half dozen or so. The look was one Rodney had never seen in another man's eyes before, and never would again, universe willing.

Carson was out of breath and put a hand on Rodney's shoulder to steady himself. "Tell me you are not firing upon those ships."

"Of course we are. Why wouldn't we be? What's going on, Carson?"

"Rodney, you must radio Colonel Sheppard at once. Tell him to stop! We cannot get through to him on Earth!"

"Carson, slow down! Why aren't you down there in the chair?"

"Cause those bloody bastards threw me out, that's why!" Carson bellowed, capturing the attention of the people above them. "The Wraith have been culling! The Hive's you're destroying are full of people!"

Many years later, when things had finally calmed down and the world started to look as if it would actually survive, Rodney McKay saw a movie he really didn't care for all that much. It was one of those artsy-fartsy films that Diane would drag him to every so often in an effort to feel normal again. There was one line of that movie that had always stuck with Rodney and always seemed to pop into his head whenever he thought back on what happened next.

The narrator of the film had described a poem called Loss, carved into the stone of a temple. The poem had only three words, but the poet had scratched them out. "You cannot read Loss," the narrator had intoned solemnly. "Only feel it."

After he'd uncovered what the IOA had done, the SGC had sent an archivist to his office to document what had happened next in his own words. Rodney had tried very hard to explain it to that poor girl who came over to his house with her little voice recorder. Tried to tell her what it was like the exact moment he knew the world would never be the same again.

But the poet in the temple had been right. There were no words to describe what it felt like to have the very air stolen from your lungs. Explain that ache in the chest Rodney got the moment he turned around and saw that look in Woolsey's eyes. The one that confessed he'd been in on it all along. There likely never would be any to adequately detail what he was feeling as he turned on his heel and headed to the control chair room, Carson and a handful of Marines sent through the gate to stop them, chasing them through the city as he fought to get to John before it was too late.

Rodney was first and foremost a scientist. He would spend considerable amounts of his time and energy in those years following the Wraith War just trying to make sense of what Woolsey and the IOA had done. He would deconstruct the events leading up to that one impossible moment again and again. Searching each one for the connections they shared at the molecular level. Nearly driving himself mad in the process because there was no rhyme or reason to any of it. No scientific formula to help explain away the sheer madness of the realization that the thing that had destroyed all of their lives was nothing more than greed and a handful of men who had forgotten what it was like to be human.

"You got awfully quiet," a tentative voice murmured beside him, bringing Rodney out of his thoughts. He glanced over at Sheppard to find his friend watching him closely.

What had they been talking about?

"So will Torren be joining the expedition?" John asked.

Oh right, his son.

"I hope so," Rodney answered after a moment. He wasn't really sure if it was the right answer. He could only imagine what people were going to say, the cracks that they were going to make behind his back when the news that he was a father finally broke. "I put in an official request to Landry a few days ago to see if he could be stationed here after he graduates ROTC in a few weeks, but I don't know if he's even seen it yet. It's not like I can sit him down and tell him the real reason I want TJ to come here."

"So you were serious?" John asked, eyebrows raised. "Nobody knows?"

"The only other person who knows besides me and Diane - and now you, of course - is Carson. And I didn't even really tell him. He was over for dinner one night and just sorta put two and two together. Once you meet TJ, you'll see why. Anyone who knew Teyla from before is going to take one look at that kid and know exactly who his mother is."

Rodney knew it was a risk asking Landry to bring TJ on at the SGC, but it was one he was willing to take. His son deserved to go back home. He deserved a chance to meet his mother's people and discover where he had come from. And hopefully reunite with his real father in the process. He owed that much to TJ at least, especially after the phone call they'd shared last night. Something was going on with TJ and it apparently had something to do with the Wraith. Rodney needed him here so they could start to get to the bottom of it.

"I lost you again," John said.

He shook his head. "Sorry what?"

"I asked you if Torren knows about all this. If he knows who he is."

"Oh yes," Rodney assured him. "Diane and I were always upfront with TJ about who he is and where he came from."

"You call him TJ?" John mused, looking a little wistful.

Rodney nodded. "It just sort of happened."

"I'm glad you were honest with him," John continued. "I always had a problem with parents that kept their kid's adoptions a secret."

"We knew it was important," Rodney said with a nod. And it was. He had always known that Atlantis would return to Pegasus eventually. He had fully planned to spend the rest of his life making sure that happened. Diane had been totally on board with the decision to tell TJ the full extent of his heritage. As soon as he was old enough to be trusted with the secret, Rodney had sat him down and told the boy everything. It had gone well, surprisingly enough, but there was one fact that Rodney had left off. One thing he knew would eventually come back to bite him in the ass. Yet another reason why he was glad he'd shared everything about TJ with John.

Rodney had been avoiding the subject for nearly 18 years. He'd told himself a million times over that telling TJ about his biological father was the right call. But no matter how hard he tried to psyche himself up for it, Rodney McKay had never been able to look his young son in the eye and tell him that his father might actually still be alive.

"I might have left out one minor detail…" Rodney admitted, shrinking a little under the penetrating gaze John threw at him.

"Oh?"

"TJ may think that his father is dead."

John sucked in a breath. "Oh man, buddy. That could get dicey."

"Tell me about it," Rodney muttered, letting out a breath. He was no fool. He knew the minute TJ got back to Atlantis people would immediately know what he had done. It would only take one ignorant person asking TJ why he wasn't more excited about going back to Pegasus to look for his father to blow the whole thing out of the water.

Rodney had been protecting his son from that particular heartache all his life, and TJ was old enough now to deal with the fact that Kanaan was alive. Yet Rodney still couldn't bring himself to do it. He couldn't get over this fear that TJ would hate him. And worse yet, that he would want to leave Rodney for good and return to a life with his biological father. Perhaps Sheppard could help him come up with a way of telling TJ that wouldn't devolve into tears and a shouting match.

TJ and John were going to hit it off famously. Rodney could tell already. They were cut from the same cloth, and he was going to have to milk that connection for all it was worth.

"Well, think of it this way," John suggested, leaning an elbow against the countertop. "We don't even know if all the Wraith have been destroyed. I know it sounds harsh to say, but if they're still out there terrorizing Pegasus then there's a good chance Kanaan might not even be alive anymore. Plus, if this kid is even half as smart as you say he is, then he'll understand why you kept that bit of intel from him."

"Wow Sheppard," Rodney mused, sitting back a little on his stool and folding his arms across his chest, "that's some sage advice coming from the man who's been moping around the SGC for the past five days blaming himself for everything that happened 18 years ago."

John narrowed his eyes almost angrily but Rodney wasn't about to back down. Carson wanted him to get John talking? Then, by god, Rodney was going to get John talking.

"You were not responsible for what happened back then. You get that now, right?"

"That's what people keep telling me," Sheppard grumbled, letting his gaze drop to the countertop for a moment.

"So when are you going to start believing it then?"

John heaved a heavy sigh and skeptical eyes lifted to meet Rodney's. "Two billion people," he said simply as skeptical gave way to mournful.

"I spent six months of my life trying to unravel all the facts about what happened that day. Did you know that?"

Sheppard shook his head.

"Mitchell and Sam... they both died so I could find out in the end that five men sat in a little windowless room in a bunker in Switzerland and decided, without conferring with their fellow IOA members or respective governments, that they would have Richard Woolsey blow all those Hives right out of the sky."

Rodney put up a hand, splaying his fingers.

"Five. And every last one of those bastards is either dead or rotting away in some jail cell where they don't even let you see sunlight.

"It's over now, and I am so very sorry that you had to go through what you did... that they betrayed you in that way, because I know the kind of person you are and how it all destroyed you. Believe me, if I could send us back in time to stop it all from happening, I would. In a heartbeat. But unfortunately for all of us, my genius brain hasn't cracked time travel just yet. All I can do is tell you this. One last time."

Rodney paused to take in a breath, Sheppard's large and baleful eyes fixated on his mouth as he spoke. "You are in no way responsible for anything that happened. No one blames you for what you were tricked into doing. I'm sorry it ever happened, but it's in the past now. It's time for all of us to let it go and move on."

Rodney let his words sink in. Judging by the look on Sheppard's face, he guessed no one, not in the 18 years he'd been grieving, had actually ever sat John Sheppard down and told him they were sorry. While Rodney certainly wasn't the one who owed that apology to him, he could at least speak on behalf of those that did.

Something shifted behind the hazel eyes that finally came to rest on Rodney, though he could still see some conflict still there. The struggle that John was having with himself over whether or not to accept or reject what Rodney was saying.

Without thinking it through, Rodney lifted his arm and ghosted the back of his hand over John's face. Over the bandages and the bruises. John closed his eyes, a single tear struggling to release from one corner of his right eye.

"I am going to fly Atlantis back to Pegasus, Rodney," John said a moment later, rather thickly and long after Rodney had removed his hand. He gave a determined nod after he said it, as if the gesture might somehow cement his resolve. It wasn't exactly a direct acknowledgment of what Rodney had said to him, but he figured it was as close to an ' okay, McKay. I'll seriously consider what you all have been trying to beat into my head for days ', as he was going to get.

"That you will get Atlantis home, I have no doubt," Rodney offered back, because he really didn't. When Sheppard got something into his head, he never gave up. Buildings could explode around him, solar flares could send him 40,000 years into the future, Wraith could suck the very life from him... and John would just keep on going.

"I just wish you could go back there and not have to carry the weight of all that bullshit around with you. It just gets in the way," Rodney finished.

"You're starting to sound like Fitzpatrick," John said with a snort and Rodney thought back on that red-headed usurper he was still trying to decide if he liked or not.

"Oh yeah," he said, "how's everything going with that?"

Sheppard shrugged. "Alright, I guess. He's pretty good with the Bantos, I'll give him that."

"Are those the sticks Teyla used to train with?" he asked and John nodded. "Ronon tried to give me a self-defense lesson with those once."

"I remember," John said with a chuckle. "You were terrible."

His friend was trying not to let his amusement show, but Rodney was smiling anyway as he let the memory play out in his head. He could recall just how ridiculous he'd looked covered in head-to-toe padding that he could barely move in.

"Fitzpatrick is using those things to help you train for Atlantis?" he asked, changing the subject.

"More like using them to put me in the infirmary," John snorted. "But yeah."

"That was mostly your fault though, you know," Rodney reminded him. "Carson said you were already on the verge of collapsing since you weren't getting enough sleep or eating properly. You're sleeping and eating now, right?"

"I am, McKay," Sheppard promised, though the smile on his face said otherwise.

"That guy… he's helping you, right?"

John paused for a moment, apparently mulling his answer over. "I think so. If anything it's nice to have someone around who wasn't there, you know? Someone who can give me an unbiased opinion. He's not even enlisted anymore, did I tell you that?"

"You didn't," Rodney replied. "I know the military uses civilian contractors all the time, but I would have thought they'd want someone from the USSF on this."

"So did I."

John took a few minutes to take Rodney through the former Petty Officer's story as well as he knew it. Rodney listened attentively, figuring he was only getting the Reader's Digest version of events, but happy to see John opening up. In the end, he got the general gist of things.

"Well," he said, "with a psychology background like that and experience working with soldiers, I can see why they kept him around. And he certainly seems to have you pegged."

"How so?" John asked a little dubiously.

"He was able to penetrate that Cro-Magnon cranium of yours and get you to open up about what happened, didn't he? Carson and I certainly weren't going to get it all out of you."

John looked sheepish. "I know, I know. I'm sorry about all that Rodney," he said genuinely. "It's not like I want to keep these things from you guys. It's just..."

"I get it, Sheppard," Rodney said, actually meaning it this time. "I've known you since the beginning, remember? And I wasn't kidding about what I said in the hallway that day after your re-enlistment ceremony. We could all care less about who you talk to, so long as you're letting someone help you with all of this crap." John didn't need to know that Rodney was secretly jealous his old friend had chosen a complete stranger over him to work through things with.

"Do you ever stop and wonder what life might be like for us if it never had happened?" John asked a little wistfully as his eyes went somewhere far off for a moment.

"All the time," Rodney admitted.

"I had this dream once that we were all standing on this balcony and looking out over the San Francisco Bay," John went on. "Atlantis was perfectly safe. I had my arm around Teyla and Ronon was right beside her and we were all just really happy... Is that stupid?" John seemed to come back to himself as he looked back over at Rodney.

"No, it's not stupid at all," he answered. "I miss them too." And in more ways than you can ever imagine , he thought to himself.

Rodney missed them because Ronon would have protected Sheppard from the IOA and never let him drop off the face of the Earth like he did. He missed them because Teyla would have done everything in her power to help Rodney bring down those responsible even though it wasn't her planet to save. The Atlantis expedition and everyone involved had lost more than just two comrades that day; the beautiful Athosian and stalwart, yet silent Sateden had fallen. For one thing, they had been the only true friends that Rodney McKay had ever known, both of them fiercely loyal (even to a scientist who talked too much and was probably more trouble than he was worth), and they had been the glue that had held them all together.

Would things have turned out differently had they not been struck down by the Wraith? Rodney could only guess. All he knew was that in the alternate universe he often let play out in his own imagination, the one where his friends had lived, everything had turned out differently.

But Rodney McKay's friends had not lived and the moment he'd seen their bodies laid out on the floor of that Hive, a hole had opened up at the center of him. For 18 years he'd been shoveling other things into that hole, trying to fill it back up, but it was still just as hollow and as empty as the day it had opened up inside of him.

"Rodney?"

He'd let himself get lost in his thoughts again and John was quietly trying to coax him back out.

"Yes?"

"What happened after I left?"

"You mean with the IOA?" he asked and John nodded. Despite his earlier fears of making things worse for John, Rodney decided to answer.

"You already know most of it... after The Great Culling the Stargate program was started right back up again. The powers that be wanted to re-establish contact with our allies in the Milky Way. They were worried more Wraith would show up. I think that's what really saved us all in the end. We were too invaluable to get rid of because we were the only ones who knew anything about Atlantis and they needed us around to help protect Earth. I used that time to start gathering more evidence on what had happened.

I know I told you that you should have stuck around to help me with it all when I came to your cabin in Wisconsin, Sheppard, but I didn't mean it. You did help. In fact, I was just about to throw in the towel when that thumb drive you sent me showed up in the mail. That's the only thing that ever convinced Carson that you might still be alive."

"I remember the day I put it in the mail to you."

Rodney remembered that too, and he still had questions for John about all that, but they were questions that could wait.

"Between the classified info Mitchell, Sam and O'Neill were able to smuggle me," he went on, "I nearly had enough to go public. But someone must have gotten wind that Mitchell and Sam were poking around and the day after they delivered the final piece of the puzzle, someone planted a car bomb in their SUV and killed them both. They were trying to scare me off but it had the opposite effect, actually.

There were rumors flying all over the SGC by that time, about what the IOA was trying to say really happened that day. But the real kicker came the moment they told me Teyla and Ronon wouldn't be given official burial ceremonies because their involvement with the Atlantis Expedition was under investigation. Those lunatics were actually trying to suggest that Ronon and Teyla had something to do with the Wraith finding Earth. They also tried to say that you knew exactly what you were doing and I wasn't about to sit around and let them run everyone's names through the mud like that. I locked myself in one of the science labs and called in every favor and contact I still had left. I tried anyone and everyone who might still be alive. I let slip that I was going to release everything to the public and not just the information about what those 5 members of the IOA had done. I was going to release info on the Stargate, Atlantis, the Goa'uld, Area 51, all of it.

Luckily for me, one of the people I managed to get a hold of was a close, personal friend of Landry's and a few days later, the first of the indictments came down. Even with the world going to hell in a handbasket, we made those bastards pay."

"Holy crap, Rodney," Sheppard declared when he finally finished. Rodney half wished he hadn't been sitting on a stool so he could collapse back against something. He hadn't sat down and gone through everything like that in a good long while and he suddenly felt exhausted. Stretched too thin, which was an odd feeling considering he also felt as empty as ever.

"You did it," Sheppard went on.

"What do you mean?"

"You saved the day."

Rodney felt his cheeks flush. 18 years ago he would have eaten the praise John gave him now right out of his hand. Today it just felt wrong to take credit for something that had needed to be done. "I didn't really have a choice."

"But you did," John kept going. "You could have walked away. You could have let them get away with everything."

"Never," Rodney said firmly. It was a thought that had never even occurred to him. Not even once during his fight to bring the IOA to justice. Not even after Cam and Sam. It was never a matter of if Rodney would prevail, but when.

Rodney glanced up to find John studying him with a strange expression on his face. It reminded him of the looks he used to catch Diane giving TJ after a particularly newsworthy accomplishment. It appeared to be something that resembled pride.

"What are you staring at?" he asked, the color high in his cheeks.

"You," John said simply.

"But why ?"

"Because…" John paused, apparently searching for the right words. "I did my job."

Rodney furrowed his brow. "I'm so confused." But John just kept giving him that look.

"You're a hero, Rodney," he finally said, and Rodney nearly fell off his stool.