Reading Time:
22 Minutes
The prodigal Colonel returns to the city and brings his dad along for the ride. Weir and Ellis have fits with varying degrees of hysteria. John and Rodney celebrate. Patrick is amused.

Twelve:
Almost before they materialized, John felt the city embrace his mind with a heavy-handed relief. He could only guess that Eliza and his father both felt the same thing since the now five-month-old let out an excited squeal and Patrick inhaled audibly. The rest of the gate room was silent as they beamed down, but certainly not empty.
In front of them was the entirety of his officer corps standing at attention. All the enlisted personnel on duty in the area and some that should have been off duty were also there, standing at attention around the control room and on the edges of the splash zone. The behavior of the military when he’d been transferred off the city had been more blatant, but he still had to swallow hard as he returned the salutes and watched probably a third of the city’s military contingent flow simultaneously into parade rest.
Major Lorne, standing somewhat in front of the other officers, spoke first. “Colonel Sheppard. Welcome back, sir.”
From her car seat, Eliza babbled excitedly but no one really responded. Not even the few civilians he could see in the control room.
Atlantis was rarely if ever a base that operated on any kind of rigid formality, at least under his command. So the adherence to formal respect hit pretty hard, and made the silent presence of his father standing beside him extremely tangible at that moment. The stiff, silent forms of Elizabeth Weir and Abraham Ellis were noticeable as well for an entirely different reason. Namely that they were both really pissed off.
John kept his attention on his XO. “Thank you Major. Have someone see to our personal items and make sure appropriate quarters and an office are set up before the end of the day.”
Lorne blinked, but immediately and smoothly had tasks assigned within seconds. Even so, no one moved.
“As you were.” The gate room sprang back to life at his words, the sound and movement drawing another excited reaction from Eliza.
“Sir,” Cadman said as she stepped up and held out a hand for the car seat. “I can take her to your quarters and stay with her until you’re done.”
He knew it was the right move. Putting off the meeting with Weir and Ellis would just increase the tension and having Eliza in the room for what would absolutely be an unpleasant discussion wasn’t really an option. Glancing once at McKay where he stood in the control room, he handed his daughter to Cadman. “She just ate and had a nap an hour ago. Her favorite toys are in my duffle.”
“I’m sure if it is not already in your rooms it will be soon.”
John took a breath and turned as the young woman left the gate room with baby in hand. The doors to the main conference room opened as they reached the top of the stairs. Ellis entered the room ahead of them, back ramrod straight. Weir followed closely behind him, arms crossed and chin up. He motioned his father in ahead of him, pausing a moment as Beckett slipped in. Rodney stepped up next to him, their shoulders brushing briefly as they both entered the room together.
The seating arrangements were rather clear in their divide, Weir, Ellis and Beckett sitting together while McKay chose a seat next to him and his father. The doors swung shut with a whisper of sound that seemed loud in the tense silence, though that silence didn’t last long.
“This is completely unacceptable,” Weir stated rather harshly. “I will be contacting the IOA in the next databurst and we’ll be addressing this ridiculous overstep.”
Ellis and Becket sat quietly on either side of her as she spat out the last few words. The doctor looked irritated but not angry. The Colonel was stiff backed and almost blank faced, but his eyes made it very clear what he thought.
McKay’s eye roll was practically audible, however, and it was all John could do to stay serious. His father didn’t seem to be concerned about such things since he looked both curious and amused. “I’m sorry, Dr. Weir, it seems you neglected to read the files that were sent to you last week. I do apologize for your confusion.”
She narrowed her eyes in a blatant display that made John doubt her diplomatic credentials all over again.
“The new members of the IOA were very clear, as was General O’Neill. Your,” Patrick paused for just a second and nodded towards her, “service has been appreciated by both the Oversight Advisory and Homeworld Security.
“But the current military threat here in Pegasus has changed the designation of the Atlantis base. As a forward operating base in a warzone staffing and leadership requirements have changed. I’m sure Mr. Woolsey and General Locke can explain further when you see them next if you still find the situation confusing.”
Weir slapped her hands onto the table in front of her. “I am the leader of the Atlantis expedition and I refuse to authorize your presence on my city.” She stood from her chair, leaning forward on her hands and glaring as she raised her voice. “You will both be leaving on the Daedalus when it returns to Earth.”
Patrick leaned back, shoulders loose and hands clasped slightly in his lap. “I myself may no longer be subject to court marshal,” he glanced briefly at Ellis, causing the man to visibly clench his teeth, “but my contract clearly states that I am to act as the civilian administrator of this city effective upon my arrival. Leaving on the Daedalus would be a breach of contract and I pride myself on being a man of word, Dr. Weir.”
Patrick sat up a little straighter, clasping his hands casually on the table. “As such, I am now the administrator of Atlantis.” He held a hand out towards John. “Colonel Sheppard is now the commanding officer of this base.”
The former Admiral’s voice was calm, concise, and utterly serious. “Yourself and Colonel Ellis are hereby relieved of your duties and no longer a part of this expedition. As ordered by the Director of Homeworld Security and the Head of the International Oversight Advisory, you are both to gather your things and report to Colonel Caldwell on the USS Daedalus for your return to Earth.”
Silence reigned for exactly three seconds. Then, Elizabeth straightened with a hiss. “Absolutely not. How dare you try to give me orders on my city.”
Patrick turned and faced the CMO, ignoring the enraged sputtering of the city’s former administrator. “Dr. Beckett, I’d like to meet with you to review your department sometime tomorrow. Please email me today to let me know when you’re available.”
“I refuse to accept this! You’re completely out of bounds and if you do not leave my city at once, there will be consequences!”
John calmly met his father’s gaze when he turned to face him. Though it was admittedly difficult to keep a straight face between the sound of Weir’s shrieks and Rodney’s open sniggering. “Colonel Sheppard, please get in touch with Ms. Emmagen and Mr. Dex as we discussed. I’m going to have someone show me to the mess hall. I’ll pick up Eliza on the way so feel free to square away any immediate issues with Major Lorne and I will see you when you’re done.”
“Don’t ignore me, Mr. Sheppard! Colonel Ellis I demand you take these two into custody immediately. This is unacceptable and the IOA will be hearing about this at the first opportunity!”
Patrick paused as the conference doors swung open at his approach. “Since my position is the head of civilian half of this expedition, the correct form of address is Dr. Sheppard. Though Admiral Sheppard would still be accurate as well. Please do make sure to use the correct title in your complaint to the IOA about the contract I signed with them.”
One of the nearby Marines stepped forward and nodded politely at his father. “This way, Admiral.”
“Thank you, Corporal.”
Weir’s face turned red and her fists clenched at her sides. Not willing to listen to any more histrionics, John glanced out the now open doors and waved over the nearest Marine. He had several options as there were rather more military than was normally stationed in the gate room.
“Sergeant.” Two enlisted men hurried into the room. “Please escort Dr. Weir aboard the Daedalus, Colonel Caldwell is expecting her.”
“How dare you!” She spit out as the Marine promptly started to usher her from the room, pushing him away with a yell. “Get your hands off me!”
“Restrain her if necessary but try not to hurt her, Sergeant.”
“Yes, sir.” He took one arm firmly but not roughly and began pulling her through the doors.
She continued to struggle, her voice getting louder and more hysterical. “Don’t touch me! Let me go immediately! I’m not going anywhere!”
John gestured towards the MP who was approaching the conference room at a jog. The man nodded and took her other arm. He activated his radio with a touch. “Daedalus, you have three to bring aboard.”
Elizabeth Weir and her escorts disappeared in a flash of light. The remaining Sergeant stepped forward when John glanced at him. He then turned and met the angry gaze of the still silent Ellis. “Colonel Ellis will also be boarding as soon as he gathers his personal belongings but I don’t believe he will require an escort, will you Colonel?”
The man somehow managed to stand even straighter. “No, sir,” he bit out before leaving at a damn near march, the Marine right behind him.
Thirteen:
Rodney practically bounced down the hallway, rambling excitedly.
“And obviously my reports on city function while you were gone were very persuasive. In the last databurst, I got an official notification from Homeworld about having the medical research department look into strengthening the gene therapy so that we had more strong ATA genes to maintain city function because they saw how right I was about needing your supergene around here to keep things running smoothly.
“Of course, Carson looked into that at the beginning and got nowhere so I doubt we’ll see a breakthrough in that area any time soon. But that just means that they have to acknowledge that your presence here is even more vital and they wouldn’t dare make you leave again!” McKay flashed a smile full of the arrogant cheer that John had grown so damn unreasonably fond of.
“O’Neill mentioned the reports. It was one of the reasons he was so irritated with me when he thought that I’d requested transfer.”
Rodney rolled his eyes. “As if you’d leave Atlantis.” He stopped in the middle of the hallway, causing several scientists to scramble around them glaring. John raised both hands is surrender when his best friend poked him in the chest with a scowl. “You better not leave again. I’ll have Ronon hogtie you and hide you in a closet on the other side of the city if you even think about it.”
“I’m not going anywhere, Rodney. I just went to a lot of trouble to get back, remember?”
Rodney glared for another moment, then nodded sharply and resumed walking. “You did a decent job of it, I have to admit. Though your dad was not included in the plan I remember you mentioning.”
John huffed at the pointed side eye. “He wasn’t. Double edged sword of parental interference, I guess. By the time I realized that he’d gotten himself read in, he’d rearranged a good chunk of his company to handle multiple government contracts with the SGC.” He ran a hand through his hair. “Next thing I knew, he was Weir’s replacement and my brother was the liaison between Sheppard Industries and the SGC.”
McKay laughed. John sighed.
“Seriously, the last few days I stayed at my dad’s David would just randomly walk into the room, shake his head at me and mutter Jesus fucking Christ, John and then walk off.”
Rodney kept laughing until they had nearly reached the larger quarters he’d been assigned before leaving. “Well, I appreciate your sacrifices on behalf of the expedition. Because based on that,” he jabbed his finger back the way they’d come, “he’s not going to suck at this.”
The door to his rooms slid open as they approached, then closed behind them both.
“Seriously, I thought Ellis was going to combust keeping his mouth shut and Weir sounded like an overheated tea kettle there at the end. It was hilarious. Definitely the most fun I’ve ever had in that conference room.”
John watched his lover drop into the couch some industrious Lieutenant had found for his suite’s living room area. Being alone with Rodney for the first time in over two months, he finally let himself look his fill. Rodney was still smirking a little, his eyes bright with amusement as he leaned back against the cushions.
He made his way over slowly, well aware that he was approaching the other man like a predator contemplating dinner. McKay seemed to notice as well, straightening up on the couch, licking his lips slightly as he watched him get closer.
“I can think of some things we could have done in that room that would be more fun.” It was meant as a tease, but the way those gorgeous blue eyes widened he was half tempted to try it. “You’re thinking about it, aren’t you? You, bent over the edge of that big table, or maybe spread out across the top, one hand holding on to each edge while I take you right there.”
Rodney blinked, then moaned as John pressed him into the couch, covering his body. He started to move against him, groaning into McKay’s open mouth as he arched up into him. “Do you want that, Rodney?” he whispered into his ear. “Do you want me to take you on that big table? Make you moan loud enough to test the soundproofing on the room?”
John pinned his arms down for several long seconds while they ground into each other. Rodney threw his head back, exposing his neck to John’s mouth. “You think you can make me moan that loud?”
The words were breathless, but clear. John pulled back, taking in the sight of Rodney panting, eyes clenched and back arched. He stood quickly, picking him up fast enough to make the other man cry out in surprise. With a hard, wet kiss, John started walking him into his bedroom.
They stumbled their way to the bed, hands scrambling and mouths clashing as they undressed each other on the way. “Challenge accepted,” John said with a smirk as he pressed two fingers into his lover.
Rodney started to laugh but his voice caught on a moan when he added a third finger. “Fuck, John. I’m ready, I’m ready.”
Taking him at his word, John rolled on a condom and slicked it up with unsteady hands before pinning him back to the mattress and kissing him hard and long. They came together, hurried, desperate. Like the months apart had left them both aching and they couldn’t wait any longer.
Rodney cried out only seconds before John groaned harshly into this mouth.
The weight of warm muscle pressed down on Rodney’s lax body while they slowly caught their breath, aftershocks trembling through them both. When his arms felt steady again, John turned them onto their sides and wrapped his arms tightly around his best friend. With his face pressed tightly into the side of Rodney’s throat he whispered, “You killed a fucking Wraith queen.”
Rodney huffed but slid his fingers into John’s hair and gave a little tug. “Shut up. You don’t get to complain about the fucked up shit that I have to do when your narrow ass isn’t there to do it for me.”
John breathed into the curve of his neck for a long moment. He pressed a kiss against the skin before he pulled back to meet his gaze. “You are not leaving my side for any mission on or off this city again. Ever.”
He rolled his eyes but left his fingers in his hair, scratching lightly against John’s scalp as they stared at each other. When Rodney broke the silence it was with a low exhale. “I didn’t expect it to take so long. Which is stupid because the trip is six damn weeks round trip and I’m not stupid, but it felt longer and I was starting to wonder if you were going to come back.”
John slowly leaned down, kissing him with all the slow gentleness that neither had bothered with that day. “I promised I’d be back, didn’t I?”
Rodney looked away, then back, looking a little flustered. “You promised to bring me more coffee too, and you better deliver John Sheppard or I’ll make you pay for it.”
John laughed, letting one hand sweep suggestively down Rodney’s bare back. “Oh, I’ll deliver all right.”
“Don’t tease me, asshole.”
“I really missed your snarky ass, McKay. I really did,” he admitted with another laugh.
Rodney glared. “My ass is not snarky. It’s a fucking modern marvel.”
John’s hand swept lower over the ass in question and squeezed. “Hmm. I think you’re right. But I should probably check just to be safe.”
They shared a heated smirk. “Safety first.”
Fourteen:
“IDC confirmed. It’s the Alpha site.”
John nodded. “Drop the shield.”
The light sparked over the event horizon, indicating that the force shield had been lowered. He waited, a little tense as Chuck informed the Apha site that they were clear to come through. It was a couple more seconds before Teyla and Ronon stepped through, the wormhole blinking out behind them.
Teyla smiled as he walked over. Ronon grunted and returned his nod of greeting. Teyla stepped forward, still smiling. “John. It is good to see you again. I was very pleased when Halling informed us that you had returned.”
He waited for her to lower her head to touch his, smiling back at her when she tilted her head towards Eliza. John easily agreed to the unspoken request and with another smile, Teyla very carefully touched her forehead to Eliza’s. The baby bounced a little in his arms and babbled excitedly at the woman. When she started to step back, his daughter threw her arms out in the universal demand to be picked up.
Teyla laughed and looked to John. He held her out, smiling when the handoff led to more exuberant noises from the little girl. Ronon’s approach only heightened the response and the large man didn’t even hesitate to take her from Teyla and hold her carefully against his chest as she babbled on. “Sheppard. About time you got back.”
John laughed. “Nice to see you too, big guy. How about lunch? They’re serving ribs and potato salad in the mess today.”
Ronon grinned. “Let’s eat.”
He led them through the city, Ronon still holding Eliza. “Where’s McKay?”
John rolled his eyes. “He’s had some big simulation running the last two days so he’s barely left the lab.” He glanced down at his watch, then activated his radio. “McKay, have you left for the mess?”
“What? I’m doing science here Sheppard, isn’t it enough that I agreed to do the team lunch thing later? Do you really have to bother me now?”
“McKay,” he said with a heavy sigh that had Teyla smiling knowingly. “Teyla and Ronon are here. We’re headed to the mess so you better put down your toys and get your ass moving.”
“What? They weren’t supposed to be here until three?”
“It’s 15:30, McKay.” There were several seconds of silence while Rodney undoubtedly checked the clock before his sulky voice came over the radio saying he was on his way.
“I see you’ve settled back in quite well.” Teyla smiled over at him, then offered her finger to Eliza when she waved her tiny fist. The baby grabbed on and didn’t let go until they ran into Rodney just inside the mess hall.
The man’s grumpy expression cleared a little when Eliza grew even more animated and demanded to be handed over. “Good idea, how are you going to grow up to be a Nobel Laureate if you get Conan cooties at such an impressionable age?”
John ignored the exchange that followed, simply steering Rodney through the line and over to the table while he continued to snipe back and forth with Ronon. “Here, sit down before you run into something.”
Rodney paused, slipped Eliza into the high chair that remained set up at the back corner table of the mess hall then quickly sat himself. John was already putting his tray in front of him when the scientist started making grabby hands.
The four team mates ate and chatted and made faces at the baby as if none of them had been gone. Before the meal was over they’d agreed to meet with his father about rejoining AR-1 and had drawn Rodney into a spirited discussion about what had been found in the Ancient database about battle tactics in the Alteran’s war with the Wraith.
By the time they were all leaving the mess hall together he and Ronon had annoyed McKay into assigning a few scientists to comb a new section of the city for a laser sword type weapon John had found mentioned in a set of ten thousand year old war records.
Not a bad afternoon at the office.
—
In the two weeks that they had been on the city, John and his father had developed the habit of having a meal together nearly every day. Usually, it was lunch since their offices were quite close and it was easy for one or the other to stop by to touch bases and have a quick meal.
The last 48 hours however had been full of meals taken on the go or in stolen bites here and there as the city scrambled to deal with a series of ridiculous emergencies only Atlantis was capable of producing. As a result, conversation had been stilted as exhaustion caught up with them both, but they’d finally managed to sit down and eat together.
John stared at his half full plate, pretty sure he was too tired to eat it.
“For someone who detours to the science labs twice a day to make sure the CSO has eaten, you don’t do a very good job at keeping yourself fed.”
John looked up to find his father lifting both brows in a rather judgmental expression.
“Eat, or you’ll feel like shit when you get up tomorrow.”
He kind of wished he had the energy to roll his eyes. Instead, he forced himself to finish the lackluster meal without falling asleep. Just as he was setting down his fork and dreaming of kicking his dad out of his quarters so he could put the baby to bed and sleep for the next eight hours, Patrick cleared his throat.
“You should invite McKay next time.”
John blinked. “What?” Eliza babbled loudly for a moment, and he looked over at her before returning his attention to his father.
“Next time we eat in your quarters, you should invite McKay to join us.”
He blinked again, not sure if it was his exhaustion making it hard to understand or if it was his father’s exhaustion making him not make sense. “What?”
Patrick sighed and leaned back in his chair. “Working together is one thing, but I think it would be appropriate for me to get to know McKay in a less professional setting, don’t you?”
“What?” John asked for the third time, swallowing past the sudden nerves swirling unpleasantly in his chest.
“Well, shouldn’t a father want to get to know his son’s best friend?” The emphasis on the words best friend were barely detectable and John had nearly convinced himself he was reading too much into the situation because he was over tired. Then Patrick met and held his gaze, smirking just a little as he continued. “He is your best friend, right son?”
John couldn’t look away. He felt pinned. Trapped. He had a sudden flashback of sitting across the breakfast table from his father the morning after he’d snuck out of the house for the first time to take a girl out without telling his dad he was going out on his first date. He let his breath out in a slow, controlled exhale. “How did you know?”
Patrick looked as amused as he did surprised. “Did you seriously think you were being subtle? You take him meals when he stays in the lab too long and walk him to his room when he stays up working half the night. Everyone automatically leaves the seat next to him open for you and vice versa because neither of you ever sit beside anyone else.”
John shrugged, leaning to the side briefly to flick on one of the animated mobiles set up beside Eliza’s play mat. He couldn’t dispute his father’s words, but really he and McKay had been like that since almost day one.
“You rarely spend your off-duty time with anyone else. He’s your first choice for watching Eliza no matter who else is available. Neither of you are more than two feet apart if you’re in the same room. You two have no personal space as far as the other is concerned and you’ve spent most of your life with an ironclad don’t touch me bubble around you.”
“Well, yeah,” John waved a hand dismissively, smiling down at his daughter for a moment when she made random noises at her mobile. “It’s McKay. He’s, he’s team.” When Eliza banged her fist against the ground where she was enjoying some tummy time on the play mat Teyla had given her, he distracted himself by reaching out and handing her one of the toys she’d thrown earlier.
Patrick sat silently for a moment, then sighed. “He’s the first person you look for when you’re upset and you’re the only person who can apparently get him to calm down when he has a meltdown over something. You smile to yourself whenever he starts rambling or ranting or muttering to himself. He watches you like a puzzle he can’t stop trying to solve. You lean towards him when he talks and he leans into your touch like a grounding wire when he starts to panic.”
John watched Eliza stuff one fist in her mouth and use the other to slam her toy into the ground. He couldn’t think of a single damn thing to say. So he leaned back away from the table and clenched his fists in his lap.
His father just continued to look at him, one brow raised. “You’re feelings for each other are obvious, John. I’d like to get to know him better. So the next time we have a private family meal, invite him to join us.”
John stared back at his father, searching his face for any sign of irritation or disapproval. He found none. Even so, it took a deep breath and a fortifying glance at his daughter playing happily a few feet away for him to nod at Patrick. “Fine.”
Patrick clapped once with a satisfied smile. “Excellent.”
Eliza squealed, then babbled loudly and waved her arms at them, as if she didn’t want to be let out of the conversation.
John waited for his father to make a sarcastic remark or take back what he said. But the man just stood and cleared off the table. “I’ll head to my quarters for some sleep, I think.” He bent down and tickled Eliza under the chin. She rolled onto her back and giggled. “And I’ll see you for our playdate tomorrow little one.”
He remained silent as his dad left, then went about getting himself and Eliza both ready for bed on autopilot, reviewing the last few minutes in his head. No matter how he looked at it, however, he was pretty sure his dad, the retired Admiral, had just tacitly given his blessing. John stared down at his daughter and watched her sleep for a few minutes, then laid down himself.
Everything had turned upside down when an Ancient machine had spit out his baby and he’d been booted off the city. It had been a desperate gamble to turn to his estranged father for help. But as he lay in his quarters on the city of Atlantis, his command restored, his daughter sleeping in the next room, his father two towers away and his lover probably slumped on his desk, everything seemed like it had been worth it. Smiling to himself, John reached out and slipped his radio in his ear. He selected McKay’s channel without having to think about it.
“Rodney.”
“Huh, what?” the groggy voice replied a few second later.
“Are you still in the lab?”
“What? Yes? What time is it?”
John sighed. “Go to bed, Rodney.”
“Hmm?” The sound of an office chair colliding with something came clearly over the radio. “Oh, right. Yeah.”
The radio chimed in his ear as the connection closed. He put it back on his bedside table and finally went to sleep.
Great ending. Weir’s tantrum is fully expected as she’s not quite sane and Ellis thought he was untouchable. Glad to see everyone settling in so well.
Thank you for the great story.
Congratulations on finishing, and thank you for sharing your work. It’s a great story in both plot and characterisation, and as I have developed a ridiculous enjoyment of stories where Elizabeth Weir is driven to practically frothing at the mouth when her – naturally evil – schemes are thwarted, I absolutely love this last chapter.
A very satisfying ending.
I greatly enjoyed the thought if a spluttering, red faced Weir being hustled away protesting all the way to the Daedalus and possibly beyond!
At least military correctness made Ellis’ departure more dignified, although he had a shorter investment in Atlantis and Weir’s schemes.
Patrick seeing and overtly recognising John’s relationship with Rodney was lovely.
Great story. Thank you.
very very cool! I enjoyed the hell outta this one — SGA is my chocolate and coffee, so this was awesome!
thanks for a grand ride! <3<3<3
Lovely!
Very satisfying read. Congratulations on meeting your word target and finishing. Thanks for sharing.
Excellent story! I never was a fan of Weir and loved seeing her go. Thank you for sharing this with us.
Enjoyed the story and the ending. Thank you.
Great story and sweet ending!
Great Story