Problems and Passions

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Content Rating:
  • G
Stargate: Atlantis, Stargate: SG1

John Sheppard/Rodney McKay, Jack O'Neill/Daniel Jackson

  • Character Bashing
  • Alternate Universe
  • Challenge Response
  • Episode Related
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Author's Note:
Mt thanks to Ed Ronhia for being my beta and friend. My response to the Just Write! Trope Bingo challenge: Episode Tag

After events of 'Coup d'Etat, General O'Neill arrives on Atlantis on the Daedalus, along with Richard Woolsey. They want to speak to Elizabeth Weir about a number of issues...

Problems and Passions

The senior staff of Atlantis gathered in the gate room, and John gritted his teeth so hard he suspected he might need to visit the dentist.  He positively hated the arrival of the Daedalus and Colonel Caldwell, knowing his every action over the last six weeks or so was about to be examined in minute detail, including his part in the recent Genii Coup d’Etat led by Ladon Radim.  At least Lorne and his team were okay, if a little tired of prisons, he thought to himself, trying to find a bright side.

Beaming you down now, sir,‘ Chuck said into his radio, and John realised he must have missed the start of the brief conversation between Chuck and the Daedalus.  

Elizabeth wore her diplomatic smile and John tried to do the same – still with gritted teeth. Rodney, as usual, had his nose buried in his tablet, while Dr Beckett…looked a little vacant, if John had to describe him. I hope he’s not still thinking about that damn retrovirus.

There was a flash of white light and three men appeared on the Gate room floor.  Within seconds each of the Security Forces had their weapons levelled at the three men but, as soon as John saw the grey head of General O’Neill, he bellowed ‘General in the room!’

The entire military contingent in the Gate room, including those on the upper balcony and John himself, came to attention, the SFs lowering their weapons as they did so, even as Elizabeth called out for them to do precisely that.  

O’Neill waved a lazy hand.  ‘At ease, everyone.’

Out of the corner of his eye, John saw Elizabeth, her lips pressed tightly together, take a deep breath, clearly embarrassed by her faux pas.

‘General O’Neill, Mr Woolsey.  To what do we owe the pleasure?’ she called to them.

Jack O’Neill tipped his head to one side.  ‘Oh, you know, I thought I’d catch a ride and see this place for myself.  It’s a bit prettier than the SGC, isn’t it?’ he added, gazing around the sun-filled room.

‘And you, Mr Woolsey?’

Woolsey gripped his briefcase against him like a shield, John noticed.  He’d only met the man once, almost a year previously on their first visit back to Earth after the Wraith siege, but he was sure the man hadn’t looked quite so pale at that time.

‘I, er…’ Woolsey began, looking between O’Neill and Weir.

‘Perhaps we can come up to your office, Liz,’ O’Neill suggested and before Elizabeth could reply, he was already jogging up the staircase with Caldwell and Woolsey following at a slightly more sedate pace.

O’Neill grinned at John as he passed him, then swung round to look at him and Rodney.  ‘Don’t go too far, Sheppard, McKay.  We’ll need to have a chat with you two as well.’  He gave them both a nod, then continued on his way to Elizabeth’s office.  He stopped suddenly, almost making Weir, who was endeavouring to get past him, bump into him instead.

‘Better make it your conference room, Liz.  More room, I expect.’  He looked around vaguely.  ‘You do have a conference room?’

It was impossible to see the expression on her face from behind her, but the way her head tipped back suddenly, suggested to John that she’d jutted out her chin, possibly grinding her teeth at the same time, just as she did whenever she was annoyed at him and Rodney – which seemed to be rather frequently, now he came to think about it.

Still facing away from them, she pointed to the room to the left of her office, then turned her head slightly.  ‘Get some refreshments sorted, John,’ she ordered and turned back, not seeing the look of surprise on his face at being treated like a servant instead of the CMO of Atlantis.

‘I’ll sort it out, sir,’ Chuck told him quietly, already clicking his radio to reach the kitchens.

‘Thanks, Chuck—’ John began but was interrupted by O’Neill before he could say anymore.

‘An hour, Sheppard, McKay?’

John managed to nod at his superior officer before he could gather his wits, but O’Neill had already disappeared into the conference room followed by Mr Woolsey and Caldwell, who gave a decided smirk to John before closing the door behind him.

‘What the—’ Rodney began, and John could almost see the steam building up inside his head, ready to boil over at any moment.  Not wanting the upcoming conversation on the control deck, John grabbed the front of his jacket and towed him towards the door.  

‘Keep a lid on it, Rodney. Not in front of the kids, eh?’


They settled themselves in the corner of the mess with some coffee and Rodney immediately opened his tablet.

‘You’re not working, Rodney,’ John complained.  ‘Put it away.’

‘I’m not working.  I just…there.  We definitely need to watch this,’ Rodney returned, and a few seconds later he put the tablet between them, the screen now showing the live feed from the Conference room.

‘Good thinking.  Any idea what this is all about?’

Rodney was silent for a moment watching the screen.  ‘I’m not sure, but I wish we could get sound from in there.’

‘At least it’s in colour.’

They watched the feed in silence for a few minutes.

‘Well, whatever O’Neill’s just said to Elizabeth did not make her happy,’ Rodney commented, then looked up at John and grinned.  ‘Why do I feel as though we should have popcorn ?’

John gave a snort of laughter.  ‘She ain’t a happy bunny, is she?’

That was, perhaps, an understatement as Elizabeth’s colour had risen to the point where she was almost beet red.

‘She’s either angry or highly embarrassed,’ Rodney commented.

‘Look at her lips, Rodney.  They’re pressed together so tightly they’re almost white.  She’s angry.’

‘Huh.  I should have recognised that expression.  It seems to be her default setting when talking to me.’

They watched in silence for a little longer; then both jerked back.

‘Holy shit!’ John muttered.  ‘I thought she was going to belt O’Neill, and from the look on O’Neill’s face he thought the same!’

‘Whatever this conversation’s regarding, it’s pretty serious.  I’m not looking forward to our interrogation one bit.  Any ideas what it’s all about?  The recent trouble with the Genii when we thought Lorne and his team were dead?’

‘That was a shit storm for sure.  And there were some abysmal decisions made.  We should never have been in a position for the Genii to capture any of us, let alone you,’ John told Rodney.

‘What about you?  You’re her Chief Military Officer?’

‘You’re far more valuable than I am, McKay, and you know it.’

‘Well, apart from the Genii it’s been weeks since we had any sort of emergency,’ Rodney said thoughtfully.  ‘Since Caldwell was last here, in fact, when you & Elizabeth were body-snatched.’

A shudder ran through John.  ‘Urg!  Let’s not talk about that.  I can’t believe I allowed her to talk me into it.’

A thoughtful look passed over Rodney’s face.  ‘D’you think it might be about that?  We’re lucky it ended as well as it did.’

John frowned. ‘How’d you work that out?’

‘Somebody could easily have been badly injured.  She got too close to what was, to all intents and purposes, an unknown artefact even though both Carson and I warned her.  We all know there’re rules and regulations about that sort of thing.’  

John opened his mouth to speak, but Rodney ploughed on.

‘She has this obsession with ascension, you know.  She was furious that you got to go into that Cloister place.  I wasn’t entirely sure she’d actually come back to Atlantis with us when we came to your rescue, you know?’

‘Really?’  John screwed up his face as though in pain.  ‘She wanted to stay?  Because it was safe from the Wraith?’

‘Maybe, but mostly because she wanted to learn how to ascend.  When we, the team and Carson, were about to go through the dilation field, I said she ought to stay behind, but she insisted on going with us.  I think if those people you met in there hadn’t ascended right after we arrived, we’d’ve had a hard time persuading her to come back here with us.  That’s why she got so close to Phoebus, I think.  In the hope she was an Ancient who could tell her how to ascend.  It was all about ascension for her.’

‘Really?’ John repeated, shaking his head.  ‘My six months in the time-dilation field were probably the worst months of my life, and I’m including the three months I spent as a POW in Iraq!  And, now you mention it, she’s cornered me more than a few times to ask me how Teer’s people reached ascension.  She is fascinated with it.’

Rodney nodded.  ‘Radek and I get a weekly report on who accesses what on the Atlantis database although I tend to ignore it.  Radek, though, keeps commenting on how much time Weir spends searching for information about ascension.  She’s completely obsessed with it.’

‘I thought—’

They were interrupted by their radios activating.

‘Colonel?  Dr McKay?  General O’Neill is ready for you now.’ 

‘Roger that, Chuck.  We’re on our way.  Sheppard out.’  John got to his feet and stretched.  ‘Might as well go and see what this is all about.’

‘Well, it was nice knowing you if it all goes south,’ Rodney told him with a wry smile.  ‘And this is Atlantis.  When doesn’t it all go south?’


There was no sign of Elizabeth on either the control deck or in her office.

‘Dr Weir said she was going to get a drink,’ Chuck told them as they appeared.  ‘I’m not sure why as there’s water and coffee in the conference room.’

Neither Rodney nor John commented, but John was pretty sure that coffee wasn’t what Elizebeth was seeking.  The two men entered the Conference room, and the General waved to a couple of seats opposite himself, Woolsey, and Colonel Caldwell.  Rodney ignored his wave and went directly to the coffee.

‘C’mon, Rodney,’ John sighed.  ‘You just had half a carafe in the mess.’

‘You know my body doesn’t run on blood alone,’ Rodney retorted, but as he took his seat next to John, he placed a cup of coffee in front of his friend.  He took a sip of his own coffee and surveyed the three men on the opposite side of the table.  ‘Well?  What’s this all about?’

Jack tilted his head.  ‘I’m pretty sure we’re meant to be asking the questions, McKay.’

‘Then get on with it!’

Before Jack could reply, Mr Woolsey cleared his throat and shuffled the large pile of files in front of him.  ‘The IOA has requested that I perform a review of the city and its senior staff.  General O’Neill is here as some of the questions are related to military matters. Colonel Caldwell is here…’  Woolsey paused and frowned.

‘To act as an independent observer.’  O’Neill was definitely smirking.

Woolsey made a neutral sound and shuffled his papers a little more.  John couldn’t help wondering why he had actual files when a laptop or tablet would have been much more convenient.

‘When contact was initially made between Atlantis and Earth, a large amount of paperwork was transmitted to the SGC, including mission reports and messages from the Expedition members to their families.’  Woolsey paused, and after a moment, John nodded, realising that a response was required.

‘Yes, yes!’ Rodney snapped.  ‘Can we get on with it?  I’m a very busy man, you know.’

If John hadn’t known Mr Woolsey was a man who appeared to lack emotions, he’d have thought he was giving Rodney the stink eye.

‘Now that the IOA has had sufficient time to review them properly, we’ve noticed the mission reports and After Action Reviews vary greatly between which personnel wrote them,’ Woolsey continued.  ‘Yours, Colonel Sheppard, are brief to the point of absurdity, containing no personal opinions whatsoever.’

‘Which exactly how the military taught him to write them,’ observed O’Neill, slouching back in his chair.  ‘We don’t want him to get all emo on us.’

‘The IOA, however, do want to have his opinion,’ Woolsey told him.  ‘Especially if it differs from his superior.’

John narrowed his eyes.  He had an idea where this was going.  Where most of my reviews had always gone, he thought with a sigh, more than a little hurt as he’d thought O’Neill was different from his other commanders.

‘As head of Homeworld Security, I’m Sheppard’s superior,’ Jack told Woolsey, surprising John.

‘Dr Weir—’

‘Is the leader of the civilian population on Atlantis,’ O’Neill finished.  ‘Sheppard may report to her, but she’s not in his line of command.  In military matters, his is the final word on Atlantis.’

Now isn’t that interesting?

‘Is this some sort of performance review?’ Rodney demanded.  ‘Because it’s highly unprofessional to have me sit here while you’re all passing judgement on John.’

‘It’s not that sort of performance review,’ O’Neill returned.  ‘We’re not here to go over all the decisions Sheppard’s taken or not taken,’ he added pointedly, looking at Woolsey with a frown.

Woolsey sighed.  ‘I brought up the matter of personal opinions because the After Action Reviews relating to the nanovirus episode, for example, are each very different.’

‘Because we all saw it from different angles,’ McKay said slowly and carefully, as though speaking to an idiot.  ‘I was actually in the lab, Weir—Elizabeth was in the control room, and Sheppard was…everywhere, it seemed, including risking his life in what amounted to a nuclear explosion to save us all!  Or did you miss that bit?’

Woolsey sighed again.  ‘Dr Weir detailed the argument she and Colonel Sheppard had over his breaking of quarantine, but the Colonel didn’t mention it at all.’

Opening his mouth to defend himself, John wasn’t fast enough.

‘What part of ‘saved us all’ are you having difficulty with, Mr Woolly?’ Rodney demanded.  ‘If John hadn’t broken quarantine, most of the non-ATA people on the city would be dead!’

John wasn’t at all apologetic about the elbow he dug into Rodney’s left arm.  ‘It’s Mr Woolsey, Rodney.  Play nicely.’  And don’t make the nice man send us back to Earth.

‘I’m more concerned that Dr Weir argued with Sheppard in the first place.’  O’Neill flicked his pen between his fingers idly.  ‘Anything to do with the security of the city is a military matter, and she should have let Sheppard take control of the situation from the start.’

‘As I understand it, Colonel Sheppard wasn’t wearing his radio,’ Woolsey said severely.

‘I was in the gym!’ John protested.

‘And we do have an internal radio system which Chuck offered to use to call for John, but Weir refused to listen to him.’  Rodney was becoming angry.

‘Calm down, kids,’ O’Neill told them all, making the ‘down’ motion with his hands.  ‘Mr Woolsey, I thought we were in agreement over why we are here?’

The colour rose in Woolsey’s cheeks.  ‘I was merely trying to establish the whys and wherefores of the situation, General O’Neill.’

‘Well, don’t!’  O’Neill turned his attention to McKay.  ‘In retrospect, how do you think Weir has performed under pressure?’

‘Badly,’ Rodney said immediately.  ‘She either takes no time to think about what to do, as she did with the nanovirus, or she takes too long like she did when John wanted to rescue Colonel Sumner.’

O’Neill’s eyes narrowed.  ‘I’ve not heard about that.  Only what happened after Sheppard went back for Sumner.  What happened, McKay?’

John tried to respond instead of Rodney, but McKay didn’t give him the chance to speak.

‘I was standing right by both Sheppard and Weir and heard everything,’ Rodney told O’Neill.  ‘Even after they went out onto the balcony after the city rose as the door didn’t close after them.  John wanted to mount a rescue immediately, but Weir wouldn’t allow it.  She wanted to negotiate.  Negotiate with things that eat us, would you believe!  John told her it was the right thing to do, but she still refused.  It was well over an hour later that she finally agreed, but by that time it was too late to save Sumner and one of the Athosians.  As far as I’m concerned, she’s responsible for Sumner’s death.  Not John.’

John gave him a feeble smile, hating the pain which still ran through him when he thought about having to shoot Sumner in the head.

‘But Colonel Sheppard is responsible for waking up the Wraith,’ Woolsey stated.  ‘That is—

‘Actually, he’s not,’ Rodney interrupted.

‘He’s not?’

‘I’m not?’

John glanced at O’Neill as they spoke at the same time.

Rodney frowned and looked between John and O’Neill.  ‘Why don’t either of you know that?’

‘Know what, McKay?’ O’Neill demanded.  ‘I have no idea what you’re talking about.’

‘But…’ Rodney looked thoughtful for a moment.  ‘That bitch!’

‘McKay!  Focus!’ John snapped.

‘I was with her when Eldon told us.’

‘Told you what!’ O’Neill demanded.  ‘For fuck’s sake, McKay.  And who’s Eldon?’

‘He’s the scientist we rescued from Olesia.  The planet with the island prison.’

‘Yet another native you brought to Atlantis without permission,’ Woolsey said in irritation.

‘They were left by the Stargate for the Wraith to feed on!’ John protested.  ‘The other prisoners escaped through the gate, but Eldon wanted to come back with us.’

‘And he’s more than proved his value to the expedition,’ Rodney added.  ‘The man’s a genius with electronics and explosives now he’s got more than trash to work with.’

‘Get in with it, Rodney!’ John told him, giving him a swift kick on the ankle.

‘Ow!’  Rodney glared at him for a moment then sighed.  ‘Eldon said that as soon as Earth was mentioned to the Keeper, the one John killed, all the Wraith woke up.  They’d been searching for the place the Ancients had escaped to for ten thousand years, and as soon as the Keeper was able to pull the details about Earth from Sumner’s head, she knew exactly what it was, and when the Keeper knew, the rest of the Wraith did too, and they all woke up.’

‘But how did this Eldon know that?’ O’Neill demanded.

‘He was sent to the island prison because he knew too much about the Magistrate – the head of Olesia, that is.  The Magistrate had an arrangement with a particular Wraith commander to provide him with enough ‘food’,’ Rodney made air quotes with his hands, ‘in exchange for not culling the city proper.  When Eldon found out about this agreement he was suddenly accused of murder and sent to the penal colony on the island.  I expect the Magistrate hoped he’d be taken by the Wraith before he could tell anyone else what he knew.  He’d overheard the Magistrate and the Wraith commander talking about the new feeding grounds, and how all the Wraith knew about them but didn’t know exactly where they were.  But the point is, Weir was with me when Eldon told us this.  Weir told me she’d tell John and you, O’Neill, about the waking the Wraith thing.  She said I was too blunt to talk to you about it sensitively, and John’s always carried so much guilt about Sumner and waking the Wraith anyway, and….Weir said she’d tell you both,’ Rodney finished, with a shrug of his shoulders.

‘Well, she didn’t!  I’ve spent the last two years crucifying myself over waking them up and condemning the entire Pegasus Galaxy.’  John sat back and closed his eyes tightly.  An immense pressure had lifted from his shoulders, pressure he hadn’t even realised he carried.

‘She told me several times that your guilt made you unsuitable to be military leader, John,’ O’Neill said quietly.

At this, both Rodney and John swiftly turned their heads to face him.  ‘What?’ John demanded.  ‘But…’

‘I was there when she said it the first time,’ Caldwell nodded, speaking for the first time.  ‘And she’s said it to me since as well.’

‘But…She…she said she was the one who pushed for my promotion,’ John managed to say, confused and hurt, almost everything he believed in since arriving on Atlantis turned on its head.

‘That was me,’ O’Neill told him gently.  ‘You’d managed to keep them all alive for a whole year, son.  You deserved the promotion and the position of Military Commander of the city.’

John couldn’t help glancing over to Caldwell at this comment, but, somewhat unusually, Caldwell smiled at him, and John felt a sudden unease.

‘You’re smiling,’ Rodney blurted out to Caldwell.  ‘Why are you smiling?  You never smile.  You hate John.  You want his job!’

‘Shut up, McKay!’ John hissed, seriously thinking about banging his head on the table, that or his own head.  Either would work.

‘I don’t hate him,’ Caldwell returned.  ‘Nor do I want his job.  I fly a spaceship every day!  There is no better job than that.  I dislike Sheppard’s sloppiness sometimes, and I’m frustrated with the fact that he’s the only Lieutenant Colonel in the US that hasn’t been to War College, and he desperately needs that knowledge to work efficiently, but I certainly don’t dislike him.’

‘Wait; what?’ John felt even more confused.  ‘I thought you couldn’t go to War College unless you’ve been invited?’

‘You have been invited, several times,’ O’Neill said in exasperation, glaring at Woolsey.  ‘The IOA has always made a point in refusing you permission to leave the city for more than a few days.  Your induction to War College would take four weeks.  Add in the extra six weeks to get to Earth and back again, you’re talking about almost three months, and they’ve refused to allow it.’

‘Even though you’re his superior and not them?’ Rodney asked.  

‘You’ve got to pick your battles, McKay.’

‘Dr Weir has assured us that the city will not function if Colonel Sheppard is away from Atlantis for that much time,’ Woolsey said severely.  ‘The IOA cares about the welfare of the residents on Atlantis even if the Air Force doesn’t.’

‘That’s utter crap!’ Rodney snapped.  ‘We’ve got any number of ATA positive people now.  If it were me away for three months, I could understand it.  I am the—’

‘Smartest man in two galaxies,’ John finished for him.  ‘Yeah, we all know.  Ad infinitum.’  He wasn’t surprised by the elbow-dig into his side.

‘Are you saying Dr Weir is incorrect?’ Woolsey demanded.

‘I’m saying she’s talking absolute bollocks,’ Rodney snapped.  ‘I think the city would certainly suffer if John were absent for much longer than three months, so don’t get any ideas about reassigning him.’  Rodney glared at O’Neill.  ‘He’s the strongest gene holder we’ve found, and he has a connection to the city that’s almost uncanny.’

‘Explain that.’

‘Yeah,’ John repeated.  ‘Explain that!’

Rodney sighed.  ‘You…you often know before something bad happens on the city, that it’s about to happen.  Like…like when the power in that lab out on the North Pier began to overload.  The scientists working in the lab had no idea there was a problem, but you knew and ordered them all to evacuate before it could explode, and you also knew exactly where to point me to sort it out.’

‘A laboratory almost exploded?’ Woolsey repeated.  ‘There was no report about that.’

‘Because it didn’t explode.  If we wrote reports about what didn’t happen on Atlantis, we’d never get any work done!’

‘But the IOA needs—’

‘No, they don’t.’  O’Neill stopped him before he could get any further.  ‘McKay’s right.  It’s bad enough writing the reports about what has happened.  If the IOA wants to know exactly what happens each and every day, one of ’em’ll have to come to Atlantis full time.’

Mr Woolsey paled, suspecting, John decided, that if anyone were sent to Atlantis on a long-term basis, it would be him.  

Woolsey, however, wasn’t about to give up.  ‘What if we supplied administrative staff to help with the reports?’

‘No,’ John said bluntly.  ‘The only way they could write the reports would be by actually being in one of the bad situations we frequently have out here.  You can send a scientist to take notes if McKay agrees, but I’m not prepared to risk my men, who’d have to protect him or her, by having someone with no military or scientific knowledge, and who doesn’t know how to act in an emergency on my city.’

‘It’s not your city, Colonel Sheppard.’

‘Actually, it is.  Or as near as damn it,’ Rodney retorted.  ‘John’s DNA is so close to the DNA profile of the Ancients we’ve found in the Atlantis database that his mother or father could have been Ancients.  And Weir wasn’t at all pleased when we found that out!’

Jack O’Neill gave a snort of laughter, and even Colonel Caldwell was grinning. Woolsey, however, wasn’t amused.

‘Dr McKay.  You are not under the protection of Stargate Command, and I advise you to watch—’

‘Yeah, he is.’

Woolsey turned to look at O’Neill so quickly John thought he might have whiplash.


‘McKay’s been contracted to the Stargate programme since, what? 1998?’

Rodney nodded.  ‘I joined Area 51 April 1998, but I’ve been under contract to the US government in one way or another since I was 19 and had just finished my second PhD.’

‘His contract with us overrides that,’ Woolsey said primly.

‘Nah, it doesn’t.’

‘There was a clause in my contract for Atlantis which keeps me in the employ of the SGC,’ Rodney told Woolsey, a little too gleefully if John was honest.  ‘All of the scientists who came from the SGC or Area 51 have the same clause.  Didn’t you read them all, Mr Woolsey?  Tut tut.’  Now there was no doubt of the glee!

‘But…That must be changed immediately!’ 

‘No can do, Woolsey,’ Jack told him.  ‘I’m not having my people be under the control of some International outfit who could order them to do God knows what.  Dr Zelenka, for example, is still wanted by the Russian government after defecting from Czechoslovakia.  Now, while Yuri Chekov is the Russian IOA rep, there isn’t a problem, but if he were to be replaced, or if one of your cabal decided to do some underhand dealing, I can’t be so certain.  The scientists you appointed for Atlantis are all contracted to you, but the rest are mine.  Except for Kavanagh, maybe.  You can have him if you want.’

John tried valiantly not to laugh, but Rodney didn’t even bother trying.  The atmosphere had lightened considerably, however, and John no longer felt he was under suspicion of anything.

‘Speaking of Kavanagh, though, he made a couple of reports I’d like to discuss with you both.’  O’Neill looked over to John and Rodney who nodded.  ‘He’s made various complaints about almost everyone on Atlantis at one time or another, but on a couple of occasions, I’d like your take on what actually happened.’  He paused for a moment and poured himself a glass of water, holding out the jug to the others with a raised eyebrow.  ‘The first was after the situation when you, Sheppard, got that bug attached to yourself.’

John scowled at O’Neill who grinned back at him.

‘I know, you hate those bugs.’

‘Because I almost turned into one!’

‘Hold onto that thought, but tell me about when your jumper got stuck in the gate.’

‘I can’t tell you anything, I’m afraid,’ John admitted.  ‘I was in and out of consciousness on the jumper, and was officially dead when I get back to the city.’

Woolsey shivered, but O’Neill just grinned at him.  ‘Been there, done that.  We should get some tee shirts.’

‘I don’t know much more than John,’ Rodney offered, ‘although I did hear about it afterwards.  All second-hand information, though.’

‘Go on.’

‘Weir got the scientists together to work out how to fix the jumper so we could get through the gate as we only had a 38-minute window to get through.’

Rodney gave O’Neill a curious look as he paused, John thought.  Part shame and part…anger?  He made a mental note to ask about it later.

‘Kavanagh made the very valid point about a possible power feedback in the drive manifold of the jumper which would almost certainly make the Stargate explode, and, with it, the city.  It was a low risk, but it was a risk, and he’d’ve been negligent not to mention it.  Weir pretty much tore him a new asshole, so Simpson told me afterwards.  It was embarrassing for Kavanagh and the rest of the team.  If she’d wanted to yell at him, she should’ve taken him aside to do it, and calling him a coward in front of his peers was beyond unprofessional.  He made an official complaint to me about it, and I forwarded it to Weir, but I never heard anything about it again, and as Kavanagh requested to return to Earth when we made contact, I let it go, but she was out of order.’

O’Neill nodded.  ‘And the time with the bomb on the city?’

John flushed.  ‘I hold as much responsibility for what almost happened as Elizabeth does.’

‘I hold even more, Sheppard.’  Caldwell leaned forward and gave a wry smile.

‘Not your fault, sir.  That could’ve happened to any of us.’

‘I was more concerned that nobody in the Mountain realised you had a Goa’uld in your head,’ O’Neill admitted.  ‘But the decision to torture Kavanagh was Weir’s and Weir’s alone, Sheppard.  Kavanagh was, is, a civilian, as is Dex.  I realise you were on a tight timeline, but nothing excuses torture.’

‘In all fairness, he did faint before Ronon could do anything,’ Rodney pointed out in defence of his teammate.

‘Weir still gave the order to torture a civilian.’ Jack sighed.  ‘Let’s move on to when Sheppard got turned into a bug.’

‘Almost turned, sir.  Not entirely.’

‘Almost turned into a bug, then.  I know how that came about, but I wanted your take on Dr Beckett’s part in it; either or both of you.’

John was a little puzzled as to what, exactly, O’Neill wanted, but Rodney knew straight away.

‘Before I say anything, I need to point out that Carson has been a good friend to me, to John as well, but I’ve known him longer.’

O’Neill nodded.  ‘Go on.’

‘Atlantis has been good for Carson.  He’s been able to progress with his research without much of the outside interference he’d get from grant boards and more senior colleagues on Earth.  I hold some of the responsibility as I didn’t check up on him or insist on seeing his reports until it was too late in some instances.  In other instances, like Hoff, I never got the opportunity.  By the time I knew what he was doing, Weir had already permitted him to continue, and I was shut out of the process.’

‘She is his superior, Dr McKay,’ Woolsey pointed out.

‘Not in scientific matters.  My job is to review all scientific research on the city, but I can only do that if I’m sent reports, and Carson never filed one, even after I chased him for them.  When he returned from Hoff, I told him to destroy all samples of the drug, but he didn’t, and I’ve only just learned that he’s been fiddling with it ever since.  My major concern, though, is with the retrovirus he created and which infected John.’  Rodney paused and poured himself a glass of water.  

John noticed his hands were shaking slightly and looked up at his face.  It probably wasn’t noticeable to anyone else who didn’t know him as well as John did, but Rodney was clearly upset.

‘I didn’t even know he was working on an iratus retrovirus, and—’

‘Hang on, McKay,’ O’Neill interrupted.  ‘What exactly is this ira…’

‘Iratus retrovirus.  It’s a synthesised virus produced by mixing human DNA with that of the Iratus bug,’ Rodney explained while John cringed.

‘I hate those bugs,’ he muttered.

Rodney gave him a tolerant smile and continued.  ‘Carson wanted it to turn the Wraith back to the human form they originally came from, thousands of years ago, but when the Wraith girl, Elia, stole it and used it on herself, it had the opposite effect, and when she scratched John on the arm, it had the same effect on him leading to the bug thing.

‘Carson made so many mistakes I’m not sure where to begin.  For a start, he should never have been using human genetic material for experimentation in the first place as it’s illegal in the US, although the arguments for and against it are continuing and—’

‘The Atlantis Expedition is an international expedition, Dr McKay, and the IOA gave its full approval for Dr Beckett’s research.  It doesn’t concern you at all,’ Woolsey told him.

O’Neill looked at him in surprise.  ‘McKay’s the CSO.  As per the Atlantis Charter, all research projects are under his purview.’

‘With what you’ve told me about his contract,’ Woolsey snapped, ‘I think the Charter is dead and buried!’

An expression of shock and surprise flashed across O’Neill’s face, then he grinned.  ‘It’s all about what’ll stand up in court,’ he told Woolsey.  ‘And with your background, I’d’ve thought you’d understand that!’  He turned his attention back to McKay.  ‘Go on, Rodney.’

Wow.  O’Neill’s just picked sides! 

Rodney nodded and shot Woolsey a poisonous glare.  ‘Regardless of whether Carson should be doing these experiments or not, I think we can all agree that he should never have taken a sample of the retrovirus off-world in an unlocked case!’

Rodney 1, Woolsey nil.

‘What was even more of an issue was that…’  He paused and glanced up at John and gave him a sad look.  ‘The human DNA he used in the retrovirus was John’s DNA; that’s why it affected John so badly.  Any other human DNA would have been rejected by John’s auto-immune system.’

A black mist fell upon John, and for a minute or so he couldn’t even think.  He came too as a glass of water was pressed into his hands, and he felt the weight of Rodney’s arm across his back.  It was a further couple of minutes before he realised that O’Neill was crouched at the side of him, gripping his knee.

‘Okay now, John?’ O’Neill asked him gently, the tone of his voice and use of his forename shocking him more than the words the General used.  He managed to nod and took a gulp of water.

‘I’m so sorry, John,’ Rodney told him, still essentially hugging him.  ‘I found out a few weeks ago but didn’t know how to broach the subject with you.  I…’

”S fine, Rodney,’ he muttered, straightening his shoulders and forcing Rodney to remove his arm.  ”M’fine.’

O’Neill patted his leg and groaned as he stood up.  ‘Too old for kneeling,’ he said, stretching his back, then moving back to his chair.  

Caldwell was on his feet holding the water jug while Woolsey was still in his seat, his face as pale as the sheets of paper spilling out from his files.

‘I…I…’ he began and took a deep breath.  ‘I didn’t know that, Colonel,  please believe me.  I…The IOA would never have agreed to Dr Beckett’s research if we’d known he used your DNA.’

‘How does that make it right?!’ Rodney demanded.  ‘He shouldn’t have been using anyone’s DNA with an alien bug!  The whole experiment should never have been authorised.’

‘No, no, I quite agree, Doctor.  I…I will order Dr Beckett to destroy all his current experiments and to begin again with—’

He broke off as O’Neill slapped his hand down on the table.

‘Carson Beckett will be beamed up to the Daedalus immediately and will return to Earth with us.  All his research is to be destroyed.  Rodney?  Will you take care of that?’

Rodney nodded, his surprise at the use of his forename evident, even while Woolsey cleared his throat.

‘I must protest, General O’Neill.  The IOA is in charge of Atlantis and—’

‘Not anymore, they’re not.’

‘I beg your pardon?’

O’Neill relaxed back in his chair again.  ‘You knew this was a possibility when we left Earth, Woolsey.  Neither the President nor I am happy with either Dr Weir’s leadership or that of the IOA, and their reign of terror ends now!’

John and Rodney looked at each other, and then at the General in surprise and some confusion.

‘I think it’s pretty clear that Dr Weir can no longer be regarded as the leader of the Atlantis Expedition, and that’s even before we get into what happened recently with the two aliens and the Genii,’ O’Neill told Woolsey, making John and Rodney sit up sharply and Caldwell to nod in agreement.

‘That’s what this has all been about?’ Rodney demanded.  ‘You’re removing her?  Who’s going to replace her?’

‘That’s not been decided as yet,’ O’Neill said, speaking over Woolsey who was trying to protest.  ‘The entire Expedition is going to come under the aegis of Stargate Command and Home World Security.’

Woolsey’s lips were pressed together as he gathered up his files and placed them in his briefcase.  ‘I can assure you that this decision will be protested by the IOA.’

‘Let them protest,’ O’Neill told him.  ‘The alternative is to have it under the control of the UN, and I don’t think any of us wants that.’

‘And what about the access of other nations to the technology you discover?’

‘They’ll have to deal with the US directly and negotiate with us.  We’re willing to share some of it, but, to be frank, the President is wary of letting Russia and China have access to some of the things we’ve discovered off-world.’

And Russia and China wouldn’t want the likes of North Korea or parts of Eastern Europe to have access either, so they won’t want to bring the UN into it.

Rodney, however, was still frowning.  ‘How can we be certain you won’t appoint another useless leader?  Your President appointed Weir to the SGC in the first place.’

‘It’ll almost certainly be someone from the military,’ O’Neill assured him, and John saw something in his expression.

‘Colonel Caldwell?  No,’ John murmured, almost to himself.  ‘No, not Colonel Caldwell.  You, sir?’

O’Neill’s lips twitched very slightly.  ‘Perhaps.’

‘Then that means Daniel Jackson as well,’ Rodney crowed, rubbing his hands together in glee.  ‘Fantastic!  He can take over the soft sciences.  The linguists and archaeologists will be in spasms of ecstasy.’

‘I thought you’d be against it,’ Caldwell said in surprise.  

‘Are you mad?  The chance to hand off all the soft sciences?  And that we’ll finally have someone in charge who doesn’t want to negotiate with space vampires or Pegasus-Nazis?  I can’t wait!’


It was a further seven weeks before the Daedalus returned to Atlantis bearing her new Commander, and John, who’d been left in charge after Elizabeth Weir had returned to Earth, couldn’t wait to hand over the reins to a newly retired Jack O’Neill, whose final act on the city as a Major General was to promote John to the rank of Colonel, and Evan Lorne to the rank of Lt Colonel.  Rodney, too, was eagerly anticipating their arrival.  He’d already set up a lab for Daniel Jackson and had loaded a laptop with all and every piece of information about the ‘soft sciences’ on which he could lay his hands.

Further news was contained in the last database: that the policy of Don’t Ask, Don’t Tell had been fully repealed, so, at the same time as they’d sought out several apartments for Jack and Daniel to choose from, John and Rodney had combined their belongings and moved in together.  Rodney would argue that there was no combining at all.  John had contributed a tatty poster of Johnny Cash and a skateboard – which was immediately put in a locked cupboard – while Rodney had supplied the rest of the furniture, books, DVDs and a top of the range coffee maker.

He also spent a good while berating John for being hesitant about moving in together, until Lorne and the rest of his command staff combined to make him aware that no single member of the Battalion would have a problem with them living together, not least because the former leader of the Stargate Programme, General O’Neill as was, would also be living with his male partner.  John had finally agreed, and within a couple of hours, Lorne had requested permission to move in with his scientist, as had Anne Teldy.

‘It was impossible while Dr Weir was here,’ Lorne told him over beers on the edge of the pier one evening while Rodney, David Parish, and Alison Porter discussed the latest gossip from the labs.  ‘She was really against any form of cohabitation, even after Doc Z and Doc Miko got married.’

‘She didn’t want them to move in together?’ John asked in puzzlement.  ‘Not even when they were married?  Why not?’

Lorne glanced at Anne Teldy who shrugged.  ‘I’m not sure, but I suspect it was some form of jealousy.’  She gave him a mischievous grin.  ‘It was no secret she was interested in you.’

‘What?!’ John yelped, spilling beer over his jeans.

‘What what?’ Rodney demanded.  ‘What’s happened?’

‘Did you know Weir was…that she wanted…’

‘In your pants?  Yeah.  Everyone did.  I thought you knew.’

‘No, I didn’t! I—’

‘—Never see those things coming,’ the others chorused, all grinning.

John grinned and shook his head.  ‘Assholes!’


Chaos reigned supreme on the city after the Daedalus arrived.  Jack looked around the apartment he and Daniel had chosen – one with a sea view and direct access to a deck area from where he could fish – and sighed at the mess lying around the sitting room.  Their furniture had been beamed directly into the apartment, but with the merging of two households into one, clothing and other belongings had been packed in suitcases and boxes.

‘Danny?’ Jack yelled again.  Where the hell has he disappeared to, again?  He clicked his radio to the channel set up for the two of them, then cursed fluently when he saw Daniel’s radio on a work surface in the kitchen area.  Sighing, he called the control room.  “It’s O’Neill, here.  Does anyone know where Dr Jackson is?  He’s left his radio here.’

I think he might be with Dr Corrigan, one of the anthropologists, sir,’ one of the control room staff.

‘Thanks.  How do I reach Dr Corrigan?’

‘I’ll get him to radio you, sir.  I’m Sergeant Chuck Campbell, RCMP, by the way.’

‘Thanks, Chuck.  Just tell him to get his ass back here, will you?’

There was a pause on the radio, then the sound of a gulp.  I’ll get him to radio you, sir,‘ Chuck repeated.

The Ancient equivalent of a doorbell sounded as Jack signed off, and he took a step towards it before remembering where he was.  He closed his eyes and thought open.  John Sheppard was in the room and looking around when he opened his eyes.

‘No need to close your eyes, sir,’ John told him grinning.

‘Fuck you, Sheppard!’

‘You’ll get used to it, sir.’

‘You do know that ending a sentence with ‘sir’ doesn’t make it automatically polite, don’t you?’

Sheppard’s lips twitched.  ‘Yes, sir.’

Jack couldn’t help shaking his head and grinning back at him.

‘I heard you lost your geek, sir.’

Jack narrowed his eyes for a moment, then nodded.  ‘It’s because he hates unpacking.  Hates any kind of housework, come to that.  It was like an illness on SG-1.  Teal’c’s place was tidy enough, I suppose, but then he didn’t have the amount of accumulated crap we do.’  He waved his arm, indicating said crap.

‘I can have a few Marines come over to help if you want?’

‘Nah, it’ll get done.  It’s all personal stuff anyway.  I’m not keen on having my skivvies handled by everybody.’

‘Fair point,’ Sheppard conceded.  ‘I came to ask if you want the full tour and to maybe search for Dr Jackson.’

‘Yes to both, thanks.  We should start in the mess as they have coffee.’

Sheppard shook his head.  ‘The best coffee’s in the labs.  We can try there first.’


Daniel was finally tracked down to the Anthropology lab where, indeed, the good coffee was found.  Jack handed him his radio, along with a sharp injunction not to leave it behind again, and let Sheppard give him the 10 cent tour rather than the nickel one he’d had previously.  This tour included a visit to the puddlejumper bay and an offer to fly one, and, almost before he knew it, he was rising into the wide blue sky above Atlantis, a grin on his face.  

Freedom to laugh, love and fly.  This is exactly why I came here.



About Daisy May

A menopausal woman writing fanfiction as a way to delay encroaching old age, grey hair, and wrinkles


  1. Ha! This is awesome! I love Jack & Daniel ending up on Atlantis, and Pegasus being better for it because psycho-Weir gets kicked back to Earth. This totally rocks! Thanks for sharing it with us!

  2. That is lovely, I can see Jack enjoying Atlantis and Daniel, of course, will be ecstatic.
    Having Rodney in the meeting saves time as he has a tendency to get to the point and cut through the rigmarole people like Woolsey use.
    Weir had no leadership experience apart from the dubious stint at the SGC, which made little sense! She had limited experience of the military and the same for her scientific knowledge, so she was hampered when dealing with the majority of the activity on Atlantis.

  3. Lovely! Sharing for sharing.

  4. What a lovely prezzie.
    Thank you. Loved it!

  5. Great story. Thank you for sharing.

  6. Awesome!

  7. I really enjoyed this. I love it when Weir and Beckett get theirs!! Thank you 😀

  8. Great Story. Thank you for sharing

  9. Absolutely delightful!

  10. I love that Daniel’s dream of coming to Atlantis is FINALLY granted.

    And good riddance to Weir and Beckett as neither showed good judgment with their choices.

  11. A most satisfactory story! I liked all the screw-ups being brought forth and those involved getting their just desserts. I never liked how some issues were handled in the show and I relish fanfics wherein those get properly managed and its ramifications explored. So, thanks for this one! And for the Jack/Daniel. I see this pairing less and less each time. :/ Luckily, SGA fics usually still keep me reasonably well supplied with my old OTP. ;D Take care and have a good week!

  12. Fabulous story, thank you.

  13. Good story

  14. LOL! Thank you, this is lovely, WW.

  15. This was great! Thank you so much for sharing! I adore Jack bringing his special kind of chaos into John’s life. Plus, your take on Caldwell was a gift!

  16. Greywolf the Wanderer

    much fun! great to see fixits for some of the really stupid shite the showrunners came up with, lol. man, this was a hoot!

  17. Oh, this was great! I really enjoyed it!

    I love stories when Jack and Daniel end up in Atlantis. I may have cheered out loud when Jack tells Woolsey where the IOA can stick it. Elizabeth and Carson being sent back to earth was deeply satisfying.

    Thanks for writing and sharing it with us!

  18. Thoroughly enjoyed the story.

  19. Just re-reading, because I can. 🤩

  20. Lovely! Thank you

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