Disclaimer: Stargate: Atlantis and all characters therein are the property of MGM. This story is for entertainment only and the author is in no way profiting from it, nor exercising any claims to Stargate Atlantis.

Title: A Time to Heal

Author: Pyrodragon2006

Warning: This takes places after the series finale! Spoilers!

Epilogue: A Time to Celebrate

Two and a half years later—

John smiled as he set down the framed photo of his mother and sister, straightening his dress blues. He still missed them, but it was an ache no longer surrounded by the bitter taste of anger and betrayal. Time really did help heal, even if there were newer, fresher, wounds added along with the photos of Elizabeth, Carson, Kate and Jinto to his memorial shelf. Only two weeks ago, they'd come so close, too damn close, to adding another. Ironic, that he had the Wraith to thank for Ronon still being with them instead of another face captured in time in a gilt frame. The 'what ifs' still haunted his nightmares.

A glance at his watch told the officer he'd better get moving or risk being late to greet the latest set of VIPs, a task that had him wishing for a mission into a Wraith stronghold instead. With Woolsey closeted by the IOA, however, still answering their unending questions and concerns, the tour guide duties devolved to the city's military commander and second-in-command, an unavoidable evil. And he wasn't even allowed to shoot any of them anymore, though that senator really had it coming when he asked for a demonstration of a Wraith stunner. Marines were paid to be targets for the bad guys, not some curious beaurocrat.

If this kept up at the current rate of at least one tour a day, John decided as he set a brisk pace down a strangely empty hallway, he might have to resort to allowing Ronon to scaring a few visits short. With the city in a shambles after their desperate jump to Earth, fight with the Wraith super-Hive, and rather hard landing, there simply weren't enough hours in the day. In addition to the stupid tours, the colonel had his own debriefings, endless reports Woolsey would normally take care of, repairs to oversee and aid with when necessary from the Control Chair, and all of his normal duties as military commander. Granted, that last had slacked off quite a bit with their location and lack of an active Stargate, but still, the only ones busier were Rodney and Radek. John laughed softly to himself. At least his friend had stopped complaining about the force of the last landing Atlantis had made, swearing never again to allow Earth to pull away their pilot when about to move the place.

Fortunately for all three men, Teyla and Ronon had taken it upon themselves to bring meals, sit upon their friends when necessary to make sure they actually ate, and enforce at least a few hours of sleep a night or they'd have long ago collapsed. The two Pegasus natives understood too well what was driving the exhausting pace. All of them wanted the city home where it belonged in Pegasus, the unfinished work there hanging in the back of everyone's mind, taunting John with the thought of allies unprotected and the Wraith culling unchecked once more. At least with three ZPMs, returning wouldn't be a problem, albeit a bit slower than the trip to Earth since there was no need to use the riskier, faster, option.

"Sheppard! About time you got here!"

The good-natured hail jolted John from his thoughts to note the Puddle Jumper already at rest on the East Pier. Not the usual landing stop, but the IOA felt it was more impressive than the drab Jumper Bay for their guests' first look at the fabled city. The colonel had grudgingly agreed when he greeted the first batch last week, Atlantis' Control Tower rising behind him and the Golden Gate Bridge in front. Major General Jack O'Neill didn't seem to be taking note of the scenery, however. John straightened hastily into attention in front of the senior officer.

"Forgive me, sir, I was told 1400."

Crap! Being given the wrong meeting time for a Jumper bearing the head of Homeworld Security and the newly named Secretary of Defense was not the way he needed his day going! He'd already spent the last six hours in the Control Chair, a dull throb picking up beat behind his eyes. If this kept up, he'd have no choice but to slip away at some point to cajole some ibuprofen out of Dr. Keller. O'Neill, meanwhile, glared at him for a moment, kicking up John's headache another notch before snorting and rolling his eyes.

"Oh, relax. I'm not in the habit of firing people for my own mistakes! I missed a time zone when I calculated arrival time."

There was a low laugh from inside the Jumper and a second man moved into the sun, joining them.

"Considering it was Jack O'Neill in the drivers' seat, I'm just glad to get here in one piece without getting shot at!"

John smiled, holding out a hand in greeting as O'Neill nailed the other man with a wounded expression.

"Mr. Secretary, congratulations on your appointment and welcome back to Atlantis."

"Thank you, Lieutenant Colonel Sheppard; it's good to be back."

Amusement at the stiff formality of the greeting sparked in the SecDef's green eyes while next to them, the general rolled his and groaned, sounding more like a bored kid than a flag officer.

"You two are killing me here!"

Matt Sheppard grinned at Jack O'Neill's complaint, and then raised an eyebrow sternly at his son.

"I trust you left the giant ticks and insane scientists behind in Pegasus? Or should I be worried about taking another unscheduled swim?"

John's own lopsided smile appeared as he relaxed into his version of a parade rest.

"Nope, I'm afraid it's been fairly boring around here lately unless you're a member of the repair crews. Sorry. The reception is scheduled for 1430 in the gate room, as you requested, General. I'm afraid I haven't seen the decorating, I've been in the Control Chair since 0800, but Major Lorne assures me everything is per your specifications."

"Excellent."

The colonel gestured the two older men into the cooler interior of the city, deciding against taking the transporters. They had plenty of time for a walk as he'd been fifteen minutes early to meet them anyway, plus there were several points of interest along the way. Besides, he was enjoying his father's company, a slow but welcome change from their previous relationship, or more precisely, their lack of one.

Oh, there'd been bumps aplenty along that road- misunderstandings, shouting matches, and the simple miscommunication that came with trying to heal a relationship from two separate galaxies, but they'd both kept at it, finally putting that Sheppard stubbornness to good use according to John's team. It'd been a pleasure for the young colonel, once he was convinced his father was sincere, to show off his base and all they'd accomplished in the Pegasus Galaxy. It'd also given John a positive focus outside of his recent traumas, a break that both Carson and Kate had happily gone along with in those three weeks before his father returned to Earth to advise the President.

After the older man left, John had established e-mail contact, finding another unexpected benefit of the renewed relationship. There'd been no need to worry about clearance levels or leaks with his father, just a steady presence on the other end of those e-mails, someone who understood not only the weight of command, but also the unique circumstances that often defied the conventional rules. Matt had been happy for any role in his son's life, and so proud to be trusted as a sounding board that he was careful never to judge his son, giving in before the arguments grew too heated. Instead, he treated John as a fellow officer seeking private advice, and asked his own questions in return, still not all that comfortable in his own role as presidential advisor. That connection had kept John steady on those dark days after the loss of first Carson, then Elizabeth, and gave him the strength to keep going when Teyla was taken by Michael. It had also brought out a renewed confidence in John, giving him the comfort level he needed to grow in his command while dispelling some of the isolation and loneliness of high position that not even his team could completely dispel. It was this, more than anything else, that had brought forgiveness and true healing at last.

This had led them here, over two years later, walking the corridors of the legendary city that had at last returned to its birth place. After several minutes of silence as they passed by two work crews, Matt gestured at some of the obvious damage.

"So, how is everything going with Atlantis, John? The Senate had me busy with confirmation hearings, so I haven't been able to keep up with your reports."

"We took quite a bit of damage but nothing that can't be fixed eventually. Colonel Carter arrived this morning, which has helped a lot, even if most of the city had to change their com frequency to avoid the arguments."

John gave what he hoped came off as a tolerably amused smile, fighting against a renewed wave of exhaustion. The chair had taken more out of him than he cared to admit, especially on top of being chronically short of sleep lately. How many hours without work had he managed in the last two days? Four? And that was only in chunks of up to an hour before another call came in. Turned out O'Neill wasn't the only bigwig bad with time zones, he'd had some insist on dropping in at midnight last night. Or was that the day before?

A sharp glance from his father told him he wasn't hiding the fatigue as well as he'd hoped. Damn! The last thing he needed was to give the impression he didn't have time for the reception honoring a Cabinet level Secretary. Especially when said secretary was his occasionally rank-touchy father! Besides, if he kept this up, one or both of the men with him were likely to sic Beckett and Keller on him!

"And how have Teyla and Ronon found Earth? Taken them to see the sights yet? I know that Ronon didn't see much when you were here last year for your grandparents' funeral."

John struggled to maintain a neutral look, mind racing to figure out where the hell his father was going with this. Was he baiting him? Sure, he'd had to leave his mother's parents' wake shortly after arriving, but his father knew damn well it was because of a Replicator loose on Earth! The job came first; Matt had drilled that relentlessly into his head as a child.

"Ah, no, not yet. "

How to phrase this so that it didn't sound like a complaint to O'Neill?

"The repairs and everything plus visitors have kept us all fairly busy. Teyla has Torrin and Kanaan with her, too, and Ronon's been helping break in some new international military members the SGC sent over."

O'Neill let loose a low, wicked chuckle.

"Emphasis on 'break' from what Teal'c tells me. "

Matt laughed, smirking in agreement, and John relaxed, glad he'd successfully dodged that one only to have the general stop him with a hand on his arm.

"Colonel, after this whole shindig is over, you're taking the next two weeks off."

The colonel's gut clenched as a thousand and one reasons that couldn't happen floated through his head. Next to him, his father was giving a satisfied nod. Shit! So that's what the whole thing was about! He wanted John to take a break without seeming to play favorites by manipulating, or possibly conspiring with, O'Neill to order it! Very sneaky.

"Sir, with all due respect, I can't leave the city while the IOA has Woolsey-"

A distinct feminine voice cut him off as Colonel Samantha Carter joined them from a side corridor, also dressed in her Class A uniform.

"That's one of the reasons that the launch of the General Hammond was delayed for a month, John. I'm not just here to help with repairs. Cam Mitchell will be joining me tomorrow, too. I think between the two of us, we can keep your city in one piece for a few weeks without you."

"Besides," Jack O'Neill smiled smugly at him, "I'm not in the habit of making requests, Colonel. That was an order. You try setting foot in this city before the two weeks are up for anything short of a Wraith invasion, and I'll… I'll… What'll I do, Carter?"

Sam ducked her head, laughing at her old team leader.

"You'll have Ronon shoot him, then Dr. Keller will sedate him and we'll ship him to northern Minnesota, sir. Not that they aren't both contemplating doing just that already, John, so I suggest you cooperate."

The Atlantis colonel narrowed his eyes at his one-time CO, but didn't say anything. Sam Carter might just carry through on the threat, even though she knew how much he hated being 'handled'.

"I'm fine."

John finally responded evenly as they approached the Gate room, ignoring several skeptical snorts.

"I'm sure Teyla and Ronon wouldn't mind some sightseeing, though. Guess I can't really say no to some time off either. It's been an interesting year. Thank you, Colonel Carter, for coming to oversee the city. I couldn't think of better hands to leave her in."

That sounded gracious enough, considering he'd just been ordered out of his own home! Besides, he could give Amelia Banks leave at the same time. She'd probably love to play guide for Ronon, which left him with Teyla and her little family. He could handle that; maybe finally get her on a Ferris wheel. With a start, John realized he was actually looking forward to this, planning activities to fill his surprise forced vacation. Plus it wouldn't take three weeks on the Daedalus to get home again!

"John…"

Matt's hand on his elbow stopped him just short of the small ramp as Carter and O'Neill moved into the large sunlit room beyond.

"I was ordered not to say anything, but I know how you react to surprises, so… The Pentagon is making some changes to the military side of Atlantis. I'll be announcing them today. You'll still be military commander, with the job you've done; they wouldn't take that away even if O'Neill and Landry weren't on your side, but… Well, you'll see. "

He walked off, leaving the pit of John's stomach dropping into his spit-shined regulation shoes. Just what did that mean? And how come no one had consulted him if they all thought he was doing such a good job? The brass usually at least warned a base commander before they pulled the rug out from underneath him, especially when the SecDef was sent to do the pulling! Face set in stony resolve to hide the broiling emotions underneath, John moved into the nerve center of Atlantis after them.

And paused in shock, turning slowly to survey the transformed space. A lectern with the seal of the Department of Defense stood in front of the silent gate, the flags of the Air Force and Marines behind it. From either side ran the flags of the nations represented in the Expedition along the edges of the platform, with the exception of the Stars and Stripes. Two of those hung from the railings on either side of the central stair case, with two honor guards, one Air Force, one Marine, by them. In the middle was seating on the floor as well as along the Control Room balconies, plus on the staircase itself, and there were still people without a place to stand or sit.

John had planned for most of the American members of the Expedition to show up, plus the senior staff, but this… It looked as though every member of the entire Expedition was here, plus a group from both the SGC and the IOA. Civilians were dressed in suits or dresses, including Woolsey standing with the rest of the senior staff, and the military were all in full formal uniform, a fact that clearly showed the multi-national nature of that contingent, normally easily overlooked unless one paid attention to the flags on the normal Atlantis uniform. The room appeared to be overflowing, a condition John had never seen it in.

As he moved fully into the room, the Atlantis military snapped to attention as one, saluting the city's military commander. Swiftly, he saluted back, as crisply as any drill sergeant- or his father- could want, puzzled by the sudden show of respect from his men and women. That hadn't exactly been in the plan, at least not the one given to him, but he spun, determined to complete his part so that he could claim the more unobtrusive seat in the front row with his team. The lieutenant colonel rigidly saluted O'Neill, Landry (where had he come from?), and his father, then walked over to the open spot between Rodney and Teyla. Beside her, he noted Kanaan, Lorne, Zelenka, Carson, Keller, and Amelia Banks, with Ronon, Carter, Teal'c, and Dr. Daniel Jackson on the other side of Rodney. As he turned smartly in place, the baby in Teyla's arms began squirming to reach out for him, and he willingly took the little boy before he could start to fuss, a move that received a slight amused smile from Matt Sheppard. Looking slightly nervous, General O'Neill approached the microphone.

"Thank you, everyone, for responding to my order- uh, I mean request- to be here today."

A ripple of laughter made its way through the room as John shifted Torrin uneasily. He hadn't heard of any order. Just how much had been happening right under his nose?

"Before I turn this microphone over to our distinguished guest, I want to personally convey my congratulations and thank you to all of you for a job well done. Not to mention for saving our collective asses two weeks ago!"

More laughter came with some scattered applause.

"Now, it is my privilege to be able to introduce to you the newly appointed United States Secretary of Defense, Matthew Sheppard."

Applause, which John sheepishly realized that he couldn't join in on with a squirming one year old in his arms. Matt raised an eyebrow at him as the older man waited out the clapping.

"Thank you, General O'Neill, everyone. Some of you may remember that this is my second visit to your wondrous city, and I must say I prefer this welcome over the last one!"

On either side of the colonel, his team tensed a bit, and uneasy shuffling was heard from behind them. If Matt had been going for a joke with that, it'd gone over like a lead balloon. Not the best start. The Secretary cleared his throat and gamely continued.

"I want to add my congratulations to the general's, along with the assurance that we know that for many of you, the job is not yet done. Soon, this city will return to its ongoing mission in the Pegasus Galaxy. To that end, the IOA has approved expanding the scientific side of the Expedition and requested a similar expansion for the military from my department, a request that the President has granted. In order to do so, however, some changes must be made, which I am here to announce. Along with added personnel, an F302 wing will be stationed on Atlantis, under the command of the city's military commander to be used at his discretion. Any and all military actions taking place in the Pegasus Galaxy will be under his operational command for the duration of the action. For those of you who are civilians, I'll translate that. Atlantis' military commander will be in overall command of all forces, including the Daedalus or any other Earth ship, during military actions. This will prevent a reoccurrence of military action taken by a ship's commander against the advice of the Atlantis commander, an oversight that was directly contributory two years ago to the loss of Dr. Elizabeth Weir."

An angry mutter from the civilians and nodding heads showed that they understood that one, all right. It had been no secret within the city that neither Weir nor Sheppard were exactly pleased with the
Apollo'
s preemptive strike on the Asuran homeworld, even if John had acknowledged the necessity. However, it left him in one giant pickle, since all the ship commanders were full bird Colonels, technically outranking him.

"In light of these changes, I have one other announcement. The IOA asked recently for your assessments and advice on the leadership of this Expedition. While the United States military alone determines the identity of Atlantis' military commander, it was agreed to take into consideration your recommendation. To a man and woman, all of you responded with just one name, which happened to match the decision of Generals O'Neill and Landry. You all came here today to honor that uniquely deserving individual as we bestow upon him the rank that is due the military commander of this fabled city, whom I have the honor of calling my son. I would ask that he now step forward, provided someone would relieve him of the youngest Expedition member first."

Solid laughter roared through the space as Teyla quickly took her son from John's arms as he stood there, dazed. It wasn't possible that meant what it sounded like! Was it? A firm hand from the other side of him pushed, starting the reeling man stumbling forward until he abruptly forced himself to pay attention to his walking so he didn't end up on the floor. John was barely aware of his team falling in behind, an unofficial honor guard. Before he had quite wrapped his head around it, the oath was administered, sealed by a kiss on the cheek from Teyla, and his silver oak leaves were replaced by silver eagles by Ronon and Rodney. His team moved to his side once more as Matt Sheppard leaned into the microphone.

"Atlantis, I give you your military commander, Colonel John Matthew Sheppard!"

The approving cheer echoed through the Tower and his ears as John found himself caught in his father's embrace.

The end. Thank you all so much for reading.