The lab was a hive of activity when Sheppard reached it. A group of their top scientists were huddled in front of a screen and, as usual, Rodney was holding court, telling them what needed to be done. His captive audience looked both alarmed and annoyed as he ran through everything still requiring their attention, his acerbic tone grating on some already fragile nerves, no doubt. But whether he was annoying them or not, they listened intently, taking down notes in various ways as he continued on with his lecture and scathing observations of the tardiness of their progress.

Sheppard was by no means a genius when it came to the internal workings of Ancient technology, or any technology for that matter, but it sounded like they'd suffered more damage than he'd first thought during their escape from Lantea. It left him wondering if they could possibly ever get the city running the way it once had, even with 'the smartest guy in two galaxies' organising and overseeing the repairs.

He hung back so he didn't disturb their discussions, some of which were rather heated as they debated the quickest and most effective ways of getting the station up and running to a point where they could make another jump if required.

Sheppard had actually been on his way to suggest they work that out, and the fact Rodney had pre-empted him worried him deeply. First Teyla, now Rodney; was no one feeling unconditionally happy to have Elizabeth back on base? Did everyone view her presence there as a threat?

The geek debate seemed to go on for an age, with Sheppard checking his watch at regular intervals and considering whether his time might be better spent elsewhere. The trouble was, everything else seemed to be going smoothly at that point. Major Lorne was overseeing all military aspects of life in the city, there was nothing untoward showing up on their long range scanners, and with Teyla supervising Elizabeth as she got cleaned up, there really was nothing else he needed to do...except read through the mountain of mission reports now piling up on his desk from the various reconnaissance trips to find potential allies and ZPMs. He decided they would do for bedtime reading since they might help to cure his insomnia. The most exciting thing he knew that had happened to any of the off world teams was getting chased back to the gate by something resembling a cross between a bear and a lion. Other than that, he figured it would all be pretty uninspiring. They'd get lucky and meet up with some useful locals soon, they always did, but right now they seemed completely alone in this part of the galaxy...at least he hoped they were.

Eventually, Rodney wound up the conversation in his usual brash manner, sending his minions scurrying away to carry out their delegated tasks. Only then did he realise Sheppard was in the room with them.

'McKay,' Sheppard said, unable to suppress a smirk as he saw the look of surprise on the scientist's face.

'Sheppard,' Rodney replied warily. 'What brings you down here? Shouldn't you be up in the control room doing 'command' things?'

'All done...everything is running like clockwork, so I thought I'd come here and get an update from you.'

'Oh, right...okay. Well, as you probably just heard, there are still several primary functions performing at less than their full capacity, so those are our priority. We need to be able to power the control chair and the shields, and although we got them up and running well enough to get us here, I think the landing may have shaken a few things loose.'

'I know, I know...I don't kiss so well,' Sheppard quipped, staring at the computer screen.

He felt McKay tense beside him, obviously unsure how to respond to that. 'Yes...well...under the circumstances I think we're all willing to forgive you moving a little too fast,' he stammered.

Sheppard rolled his eyes in the scientist's direction, arching an eyebrow.

'All right, all right, so you're better at those kinds of jokes than I am, Captain Innuendo,' Rodney admitted, firing up the program he wanted Sheppard to take a look at. 'I can get the shields up to protect about two thirds of the city so far, but the outer regions are still exposed,' he explained, setting a three dimensional diagram into a slow rotation on the screen. The shield covered the central parts of the city and extended out to cover most of the narrow walkways through to the outer buildings, but those structures themselves remained untouched by its protection. 'So, as you can see, we are currently vulnerable to infiltration or attack in those outlying sections until I can fix or bypass the circuits currently not functioning.'

'And are the sensors working out in those areas?'

Rodney shook his head, looking grim. 'Not as of ten minutes ago. Circuits all over the city seem to be dying as quickly as we can replace them. When I said vulnerable, I meant vulnerable.'

Sheppard nodded, trying to keep the image of the Asuran city ship approaching them out of his head. If even a handful of those Replicators got into the city undetected, they could take Atlantis down from the inside.

'Okay, we haven't picked anything up approaching on the deep space scans so far, but I think it might be an idea to double the security teams in those outer reaches for the time being, just to keep a visual tab on what's going on out there. I'll notify Lorne.'

'Good thinking...but there's more,' Rodney interrupted, holding up a finger to stop him. 'The hyperdrive circuits are fried and we can't fire any drones if we come under attack because the weapons system is off-line. Until I get all that fixed, we're little more than sitting ducks.'

That wasn't good. A few days ago all those things had been working. Now, as Atlantis settled into its new position in the galaxy, it seemed circuits that had held out following the damage from the Asuran satellite weapon were now giving up the ghost. 'Stay positive, Rodney. You've kept us all alive this far; I have every faith you'll continue to do so.'

Rodney gaped at him as if he was waiting for the punch line. Sheppard just clapped a hand on his shoulder to show he meant it, quickly snatching it back.

'This new-found maturity of yours is going to take some getting used to,' McKay grunted, returning his attention to the computer.

'I know. I'm not that comfortable with it myself, but it comes with the job title,' Sheppard replied, deadpan.

After toggling through a few more screens, Rodney peered up at him. 'Was there something else?'

Not sure quite how to broach the subject, Sheppard pulled up a stool and sat down at McKay's workstation. 'I was just wondering how you're doing?'

McKay stared back at him, slack-jawed and bemused. 'What? Why? Has somebody been talking about me?'

'No, nothing like that. It's just that now I'm in command here, the welfare of everyone in the city is my concern. So, I thought I should ask how you're coping.'

'Seriously? You know, this is kind of creepy...it's like you've had a personality transplant or something.'

'Come on, McKay. I'm trying to do the right thing here. Just play nice, okay?'

'Hmmm, all right. I'm good, thanks for asking. Are we done now?'

'Are you sleeping any better?'

Rodney looked terribly uncomfortable with his continued questioning, but kept up his side of the bargain. 'A little better, I suppose.'

'So you didn't sit up all night working again?'

'Not all night...no. But I do find work is the only think that keeps my mind off –' His face suddenly dropped, and Sheppard's heart leapt into his throat as he wondered what his friend was about to say. 'This new you doesn't give hugs, does it? Because, really, that would be just too weird.'

Grimacing at the mere thought of it, Sheppard slapped Rodney around the back of the head, giving him his non-verbal answer.

'Ahhh, now that's more like it,' Rodney quipped, apparently more comfortable now even if he did have to rub his head because it smarted from the contact. 'Now, if you'll excuse me, I've got a million and one jobs to do...' He turned back to his laptop and began to key in instructions.

'There is one other thing,' Sheppard ventured, watching Rodney's shoulders tense as he stood hunched over his computer. 'You went to see Elizabeth yesterday, right?'

Rodney turned back to him, nodding. 'Yeah...I wanted to tell her I was sorry about getting her in trouble with the Replicators...even though it wasn't strictly my fault.'

'How did she seem to you?'

Rodney narrowed his eyes, clearly trying to work out if Sheppard's words had some hidden meaning he was missing. 'She seemed good. Why, are you worried about her?'

'No...not exactly.'

'What do you mean, not exactly?' Rodney demanded, his anxiety mounting. 'Is she showing signs of going 'dark side' on us because that's not the kind of thing you should keep from people?'

Sheppard sighed, throwing his paranoid friend an angry frown. 'I'm the one asking how you think she is, Rodney. Did she seem normal to you?'

'Yes...I suppose. How about you?'

'Yeah...yeah. And how do you feel now we have her back?'

'Well, how do you feel?' McKay fired back at him.

'Rodney!' Sheppard growled, his green eyes flashing with anger. 'I'm trying to assess your feelings on this. If you keep asking how I feel first, you're just gonna say what you think I want to hear.'

'Oh, so now you're a psychologist, too?' McKay countered

'McKay!'

'All right, all right. I suppose...I suppose I don't feel as happy to have her back here as I thought I would.'

At last, some honesty, something he could get a handle on, and something he could understand because that was exactly how he felt, too. 'What is it that's stopping you from feeling happy?' he pressed, wondering if Rodney's concerns were the ones both he and Teyla shared.

'I don't know...' McKay whined. 'Perhaps, it's just that finding her seems to be...well...too convenient. Why did the Replicators let her go like that? Surely they could find more uses for her than dumping her on some uninhabited planet to rot or provide a meal for the indigenous wildlife.'

'Yeah...I'm having trouble with that myself,' Sheppard confessed.

They both stared at each other, Sheppard wondering what was going on inside McKay's overworked mind. He looked frightened, angry, worried, all in one great whirl, and Sheppard supposed he was feeling all those things, too, though he didn't want to admit it. He wanted to be pleased Elizabeth was alive and well, but this scenario had 'trap' written all over it.

'Do you think there might be some way of reprogramming those nanites to do what you originally planned now, you know, using materials from inside Elizabeth's body to repair the damage done in the blast.'

McKay's eyes drifted away from his as he thought about that, and Sheppard could almost see him computing the calculations and problems involved in that kind of reprogramming. 'Well, I suppose if I'm not up against a tight deadline there's no reason I couldn't write a program to do that. It would involve doing the repairs gradually and then getting the nanites to recognise when they're finished and shut down, but it's not impossible. Of course, I'll have to consult with Dr Keller to make sure they carry out the repairs in a viable way, and with the minimum disruption to Elizabeth herself, but gimme a week or two and I can probably work something out.'

'That long?' Sheppard asked, hoping this was one of those occasions when Rodney was being conservative with his estimate of time so he could look good when he did it much faster.

Rodney, rolled his eyes, his expression changing instantly to his normal scowl. 'Oh, I'm sorry to disappoint you, but brain surgery on the nanoscopic level isn't quite as simple as you might imagine.'

Sheppard rolled his eyes and counted to ten, his tried and tested way for dealing with one of McKay's fits of choler. 'You don't say. Look, just try and fix them sooner rather than later, okay?'

'And is this more important that fixing the hyperdrive, the weapons systems, or the shield generators, because, honestly, I'm not sure I should make that call.'

'Delegate, Rodney. You have a good team of people capable of helping with those other things. Use them.' He heard echoes of Elizabeth's warning to him as he spoke, realising he still trusted her more than he imagined he did

'Delegate...yes...I suppose I can do that,' Rodney nodded, scratching at his head as he tried to figure out the best person for each job.

'But before you get going on any of those things, I need your help. The IOA are keen to get to the bottom of what happened to Elizabeth while she was in Asuran hands. I'd like you to sit in on the interview, too.'

'Me? Why?' he asked, looking surprised as well as mildly concerned.

'Because protocol states there should be two members of Atlantis' crew present, and I think hearing what she has to say first hand will help you to come to terms with the part you played in things,' Sheppard told him.

He watched as McKay's jaw drop a little way. 'Oh...right...well, when you put it that way...I'll go get my Hazmat suit.'

'No. No hazmat gear. I want Elizabeth to feel as comfortable as possible when we speak to her. If we're sitting there looking like we're scared she might infect us, that isn't going to help her to relax, is it?'

'No...no...of course. You want me to ask someone to set up the recording stuff?'

'I'd appreciate that, Rodney.'

Rodney winced at the show of gratitude. 'You know, I'll be glad when we get our new commander in place. Then you can get back to normal and stop being so nice. It's unsettling.'

'Amen to that,' Sheppard laughed, hopping off the stool and following McKay out of the lab.