Chapter 50: Proud

John looked out over the ocean, foot beating steadily against the bulwark. He had been recently upgraded to a walking boot and was probably taking Carson's lifting of restrictions a little too leniently.

But he needed to get away.

Daniels and his team were still working on entirely upending the city. They had sussed out three more sleeper agents – two for the IOA and one for the Trust – that had tried working themselves in with the newest recruits. It made him want to question and interrogate every single person under his command, but he knew that wasn't realistic.

Rodney had been thrilled to get his hands on the code for the Ancient Killers and had already started backtracking some of his previous work that had been interrupted by the invasion. John had a feeling that they were going to have a fix, up and running within the next several weeks. A good thing, since nearly ninety percent of their remaining zats had all been infected. They had also gained a handful of zats from the invasion, so… it all balanced out in the end.

Alex and Lieutenant Simmons had, oddly, been inseparable for the past few days. Alex had, notably, skipped the mess after a rather disastrous attempt when some of the less circumspect Marines all but mobbed him – but Carson had assured John that he was still getting meals in his room. It was a tossup to whether that was a good or a bad thing – especially since it seemed like Alex was trying to more or less avoid everyone on base – including all the scientists.

Rumors had flown.

Wildly.

Though it had taken a while before anyone realized that the common denominator of the massacre had been Alex. He had to give his people credit that they didn't immediately believe a teenager had been the deciding factor in whether they all continued under Gregoria's leadership and killed off the existing leadership.

No doubt, Alex was trying to avoid his now adoring public.

The Marines were just as enthralled with him as they were with Ronon, the other hero of the hour that was more than happy to ignoring their adoring stares. At least one unit seemed to care about Alex's wishes in the matter and were trying to run interference.

John kicked at the ledge again.

He wasn't bitter.

Wasn't jealous.

Was… annoyed that he had been pulled into the trap, just like everyone else. That he hadn't managed to do anything to prevent it from happening again. Hadn't broken out or fought back against their captors.

Hadn't been able to, because he had been handicapped. Still was, if Beckett was to be believed. He didn't bounce back quite like he used to when he was younger.

Now, everyone looked to Daniels for leadership. Daniels for information.

It was Daniels this. Daniels that.

"Thought you might be out here, sir."

He didn't startle. Not in the slightest.

John looked over his shoulder to see Simmons – without Alex for once. There were no remaining signs of his own ordeal.

"Mind if I join you?"

John glanced up and down the pier, before waving at the empty space. "Not going to stop you, Lieutenant."

Simmons settled down with a slight grunt, before looking out over the water. The city was far enough out that none of the landmasses were visible, leaving nothing but a vast expanse in front of them

John blew out a long breath, letting his shoulders slump. He had never spent enough time around his superior officers to know how to behave – they weren't really human in his mind, though at that point he hadn't been aware of the existence of aliens. He had just always done his best to steer clear of the upper brass. It was safer that way. No reason to stand out.

The same had been true for his subordinates – there was probably a line that was being crossed here.

"Alex has told me some interesting things this past week," Simmons said, with little preamble.

John suspected that that was an understatement. There were numerous directions that Alex could've talked about – his own past, their relationship, Pilkes' strange and confusing history, even the mess with the Trust.

"I think everyone forgot about the love child rumors within the first week."

John snorted. That had been annoying, at the time, but he hadn't known then what he did now. That there actually was a shard of truth to the rumors.

Simeon reached down and grabbed a barnacle, sending a sly grin in John's direction before dropping it over the edge. The resulting crackle sent a shiver over them both and John realized just how vulnerable he was. Out here, alone.

If they had been wrong about their estimation of Simmons and Pilkes… It would be the end.

"He really does act like you though. Little things, looking back, that seems to make a lot more sense. And Dr. Beckett? And General O'Neill?" Simmons laughed softly. "I don't envy the two of you the eventual family reunion."

Right. Because that was a thing that was going to happen sometime soon.

If the rumors were to be believed O'Neill was going to be coming for a personal visit in the near future. Very near future. Though they hadn't announced the revelation with Pilkes in any official manner, O'Neill had certainly been informed of the details. And an alien somehow infiltrating the SGC for years on end… that was a pretty big fucking problem. Though it seemed he had insider information from the get go, so… maybe it wasn't quite as big a deal as it could be. Only Rodney it seemed, could outsmart Rodney.

And wasn't that a mindfuck.

"I think he's less anxious about getting sent back to Earth now."

John jerked up to look at Simmons. "Still?"

Simmons shrugged. "Seems like he's been bounced from place to place over the past couple years. And Woolsey was definitely campaigning to get him off the city permanently. Daniels taking over seems to have established some sort of stability."

John bristled at the name.

Daniels.

The golden boy in all this.

John wasn't jealous that he had been able to be there for Alex in the past. Not at all.

Just…

"You know he looks up to you?" Simmons asked, quietly.

Right.

Why would Alex want anything to do with him anyway?

Though he knew full well he had never been in a good position to raise a child… that choice had been taken away from him. All by someone who had decided they knew better.

It was sickening.

"Whatever history he has with Daniels, it was fleeting. You've done far more for him than Daniels ever has."

John clenched his teeth. He knew that. He had all but pulled Alex out of the SGC, after all. Had decide to take on the kid without knowing hardly any of his history – much less the secrets that lurked beneath the surface. That had to count for something.

But Alex wasn't talking to him.

Hadn't said anything or made any attempt to reach out.

They were like strangers once again.

And that made John feel like a petulant child – complaining that his son was ignoring him.

Simmons sighed, before slouching next to him. "Alex said you don't remember anything from… the year he was born."

"I remember my version of events – Stanford, classes, getting the test pilot posting." John picked up another of the barnacles, letting the electric shock ripple over his skin. "It just isn't reality, apparently."

And perhaps that was still the hardest part to wrap his brain around. He could acknowledge that Alex was his. DNA testing proved that. But that his own memories couldn't be trusted. That they were somehow completely fabricated? Could he trust anything that was from any of those years?

"Have you thought about the Galaran's, sir?"

"The who?" It wasn't a name he was familiar with.

"Galaran. SG-1 ran across them a couple of years ago." Simmons picked at a seam on his pants, as if uncertain about how his suggestion would be received. "General Mitchell was accused of murder, but they had used a memory device on him that essentially replaced his memories. Maybe… something like that happened to you?"

John turned and stared at his subordinate. "Just how much thought have you put into this?"

Simmons shrugged. "Alex was going stir-crazy, so I figured some greatest hits from SG-1 would give him something else to think about. Once we stumbled across that one, well…" He ducked his head. "It seemed like a reasonable explanation, except for the fact that the Stargate hadn't opened yet in 1993. But we also know that Pilkes time traveled, so it stands to reason that someone else could have as well."

John turned it over in his mind.

It was about the last thing they needed, but it seemed that nothing was outside the realm of possibility at this point.

Maybe he would have to hunt down that particular report to take a look at it for himself.

"You should talk with him."

John startled out of his musing, turning to look at Simmons who was studying him with a careful gaze. "Alex?"

"Hmm… Dr. Beckett seems to be helping him process the… changes over the past several weeks. But I've heard the stories about the Genii. If anyone understands what he's going through right now, I think it would be you."

It was awfully brave of a mere lieutenant to say.

But he was right.

And if there was one thing John had learned, was that it didn't matter the rank sometimes.

The fiasco with the Genii and the subsequent nickname of Sheppard the Butcher hadn't gone over well with some of his men. And it had gone too well with some of the others. The hero worship. The mixed awe and fear that made him feel like nothing more than a circus performer.

But he had had the shield of his position.

Alex had… nothing.

Not even the acknowledgment of his parent.

"Maybe…" John said, noncommittally. But he knew he would. He needed to clear the air with Alex. Make it clear that nothing had really changed. That all of the things they had gone through and stumbled through in the past several weeks – he was still going to do his best by Alex. Make sure that he had the best opportunities the galaxy could offer him.

It wasn't going to be easy to get through some of his stubbornness, but at least Alex came by that naturally.

Manufacturing a conversation with Alex was easier said than done. Especially since not a day later, Carson had finally released John to fulltime work. That meant catching up on the backlog of paperwork that he couldn't in good conscience shove off onto Lorne – in depth reviews of all the after-action reports and a serious look at the operational security of the entire city.

They had good reason to set up a beta site and potentially another off-world location for diplomatic meetings entirely. And there was no way John was going to let some earth-based bureaucrat dictate policy in the city anymore. Two invasions were two too many.

Of course, that meant he needed to work with Daniels and John really needed to get over his little jealousy problem.

"I hear the range is empty this time of day, sir."

John looked up blearily from the endless stack of notes he had been working his way through for the better part of five hours.

Lorne seemed to eye the most precariously stacked pile with caution. "I believe Dr. Beckett's instructions were a gradual return to duties – not full speed into the depths of bureaucracy hell. Sir." He tacked on at the end, looking contrite.

John rubbed at the bridge of his nose. "Preventing another clusterfuck isn't just going to happen overnight, Major." There were swaths of reports he needed to get through, before he could even think of presenting the proposal – no, demand – to Daniels. If they didn't have better security on the city, it was only a matter of time before another incident occurred.

And he wasn't likely to be as lucky the next time.

"Exactly, sir. Which is why you'll find Corporal Markus and Captain Summers' threat assessment from the most recent invasion riveting." Lorne said, dryly. "And that'll be in your inbox in approximately…" He looked at his wrist exaggeratedly. "Two hours. Just enough time to blow off some steam at the ineffectual reports submitted by Staff Sergeant Nunez and Sergeant Killpatrick."

John eyed Lorne skeptically, not entirely sure the man didn't have his tablet bugged. Because he had just been mulling over whether Sergeant Killpatrick would be staying on with the expedition – the man had nearly done more harm with friendly fire than the invaders had.

"And the range is within the allowable physical activities, per Dr. Beckett. Sir."

Something told him if he didn't get out of the office, Lorne wouldn't hesitate to track down Carson. Then who knew what would be imposed on him.

He sighed. One day, they were going to have to remember who the Colonel in charge was.

"Two hours?" John asked.

"Yes, sir." Lorne stepped back respectfully.

"Then, I suppose so time on the range wouldn't be amiss." At least he would get the satisfaction of taking something out. Which he wished he could do to Killpatrick, so maybe that decision had already been made. "Major Lorne, you have point with Director Daniels until I return. I expect that report in my inbox in two hours."

Lorne snapped off a salute, that almost didn't look smug, before all but ushering John out of the room.

It hadn't occurred to John that his subordinates were plotting.

Lorne's insistence that he get some time in on the range when he was becoming visibly frustrated with the reports wasn't out of the norm. Well, the range or sparring. If reports were really bad, then Lorne quietly arranged for Teyla to be available for some bantos practice. Or Ronon, in a pinch.

But it hadn't ever crossed his mind that this was a set up.

Not that he was entirely unhappy about it – things had just gotten too busy once again.

Lieutenant Simmons glanced up from where he was spotting Alex on the range, a briefly pleased look crossing his face. He tapped Alex on the shoulder, before motioning in John's direction. "And this is my time to leave. Excuse me, sir."

The lieutenant was out faster than John could process, leaving him staring in Alex's direction with confusion.

Alex carefully glanced up and down the range, before settling his gaze on John. "They set us up."

And the absurdity of it all… John couldn't help the bark of laughter. Because of course his own men thought they needed to meddle. At least, those that were now in the know. And they were apparently on a time limit – because two hours. What exactly everyone thought they needed to settle in two hours… what they could settle in two hours…

Alex reloaded a new magazine into the P90 he was holding, before nodding toward the lockers. "Got any accuracy tips?"

And maybe, maybe they could make progress.

Nearly an hour had passed going through the armory with Alex. It had been soothing in a sense – something familiar for John, routine, and some bits new for Alex. It had been a long time since John had worked with someone transitioning from handguns, but Alex had an innate sense for using the weapon. They had switched back and forth between familiar and unfamiliar, until they had reached the end of the personally allotted ammunition for the week.

Practice would have to resume another time.

From there though, they had wandered out onto the pier, shuffling barnacles to give off a little privacy. Alex was almost chatty as he talked about the project Radek had him working on – though John noted there were far fewer complaints about the complexity of the Ancient database.

John eyed Alex as they settled against the railing, with Alex going off on a tangent about the cool-down mechanism he had found in the blueprints for an early energy gun. Which… "When did you learn to read Ancient?"

Alex stopped short, mouth dropping open, before flushing wildly. "I… haven't…"

"Uh, huh." John raised a skeptical eyebrow in his direction. "Try again. Even I know Rodney hasn't translated anything about energy weapons recently – much less Dr. Z."

Alex blew out a long breath. "It just… Everything started making sense after I sat in the chair." His shoulder drooped slightly, before he set his jaw. "Don't tell Dr. McKay – he'll restrict my access to everything boring."

John snorted. There was probably good reason for that. An impulsive teenager with the power of the Ancients at his fingertips? "So you've had two weeks of these new abilities? And didn't say anything to anyone?"

That earned him a grimace. "Figured there were more important things going on."

It was a fair point. "And do you have plans to try anything out? Or just for curiosity's sake?" Because two weeks of self-control was a point in his favor.

"Only if Dr. Z or Dr. McKay signs off on it. Scout's honor."

John eyed him warily. "Were you ever even a scout?"

Alex shrugged, tuning to stare at he waves. "Ian didn't have time for it fulltime. And I don't think we stayed in the same place for longer than three months when I was between the ages of five and eight."

All teasing fell out at the moment. It felt oddly vulnerable. A piece of Alex that he probably hadn't shared in a long time. "Yeah, that… that sounds like Ian. Even if it was for work, he always loved to be on the move." Before his brother had died, John's intermittent contact had involved postcards – it was always a guess where the next one would be from.

"Nice to know they didn't entirely replace his personality," Alex said bitterly.

John chewed on his lip for a long moment, turning over the bits and pieces Alex and reports had let slip through. "I… don't think they changed a whole lot. Or weren't as successful as they thought. Ian did his best to protect you in the only way he knew how – by giving you opportunities and access to tools and skills." And John had never been more thankful for it than recently. "We would have been in a much worse situation if it weren't for you."

Alex snorted at that. "Much worse." He kicked at another barnacle. "Not everyone agrees with that though. Greg tries to help but…"

How he wished Alex could have been saved this. He was supposed to be safe on the city. That had been the entire point of bringing him out. "When the Genii invaded, there were only a handful of us left on the city. I was responsible for the deaths of over 47 of them – if you include those that hit the gate shield. After that… there were more than a few nicknames that were thrown around – Sheppard the Butcher, for one. Some people thought we should have taken them into custody. Some people thought we should've negotiated. Some people thought that an air force colonel had no business doing that sort of wetwork. That someone that violent should never have been in charge of the military on a base. That I was… corrupted for protecting our home." John blew out a long breath. Even years later, it still stung that so many had gone against him or spoke behind his back. "There will always be people who side-eye you, who question your position in this city. But the section that matters, the core that are making the decision here, know that you were the only thing standing between this city and certain destruction at the hands of the Trust."

Alex nodded morosely, not making eye contact.

John took a deep breath, before focusing on the teen in front of him. "And I'm very proud of you for that."

A/N: Hello! I swear I haven't forgotten you all! We should have one more chapter to go to tie up all the ends. Hopefully… Working full-time and a quarter makes having a life for extracurriculars a little difficult, but I am resolute to finish this story. And maybe work on part two? (Not promising anything, as it doesn't have a single word written toward it…)