It is only a hypothesis at first, a convenient (if wholly unscientific) explanation for why the lights seem dimmer, the response times feel slower, and systems that can usually be coaxed into accepting the forced interface between Earth technology and Ancient are suddenly reluctant, if not downright dismissive.
It is only a hypothesis because nobody can chart a drop in lumens or reaction time and Radek has run every test he could think of to figure out why Atlantis capriciously won't recognize the laptops in the control room or the labs without at least two reboots and lot of begging and pleading to inanimate objects that maybe aren't. It is nothing Rodney would have been able to fix, he explains to Dr. Weir when she doesn't come out and ask but looks speculatively at him, because for all of McKay's many areas of genius, getting foreign technologies to work with each other isn't one of them. It was something he had always let Radek handle, the delegation of responsibility a tacit acknowledgement (the only kind from McKay) of Radek's superior knowledge and experience.
What he doesn't say is that the problem with Atlantis is that Atlantis knows and Rodney would have been useless because he would never have admitted the problem existed.
Radek knows that Rodney would have scoffed at his hypothesis because Rodney believes without reservation that man rules machine naturally and completely and by right. Radek does not tell Elizabeth (or anyone else) that if Rodney were here, he would have turned the entire science division to the task of breaking Atlantis to the bit because he refuses to accept that Atlantis has a will to break. Even after the gene therapy took and he, too, could feel Atlantis's touch, Rodney did not alter his opinion that Atlantis was little better than a slave, albeit a highly advanced one. Radek thought it very small-minded for someone with such a big brain and he'd told Rodney so. A long afternoon of uncomfortable silence resulted, but Radek was and is still convinced even as Atlantis's moods remain opaque to him.
It is only a hypothesis because he cannot prove it by any means acceptable to any official organization back on Earth. But that does not change what Radek believes to be true: Atlantis knows that the one she holds most dear has been taken from her.
It stops being a hypothesis after Toivannen and Selikhova return from the south pier wet and frustrated and complaining that Atlantis should have been told about Sheppard right away so that she could mourn and then get back to work and stop taking her grief out on the rest of them.
Once it has been spoken aloud, the hypothesis becomes thesis becomes fact simply because, it seems, everyone has been believing it all along in the privacy of their minds. There is still no quantifiable proof, but articles of faith don't always require tangible evidence.
Atlantis knows and is grieving and Radek finds himself murmuring softly to her as he works on her infrastructure, even though he's not sure she can hear him.
Most of the time, Atlantis behaves for him as she always has, which is as if she is suffering his touch because she knows that as distasteful as it is, the reward will be worth it. But sometimes she is like a fretful child and there is nothing Radek can do to soothe her into compliance.
Nevertheless, he tries his usual array of parlor tricks and distractions he has developed because, even with the ZPM in place, Atlantis is fickle about many things and stubborn about many more. She does not like being overruled or second-guessed and if she has kept a door closed even after Sheppard has been retrieved to cajole her into opening it, she will prove restive and difficult once they have manually overridden the lock and Sheppard's most earnest mental caresses are usually only good enough to get the lights on.
Without Sheppard -- and usually now without the too-busy Stackhouse or Beckett or Kusanagi or any of the other naturally ATA-endowed residents -- to romance her into acquiescence (if not obedience), Atlantis is frequently sullen and occasionally spiteful. It is just as well that the expedition is wholly focused on the search for Sheppard's team because precious little productive investigative work is getting done. Radek is not alone in thinking that this is intentional on Atlantis's part, forcing them to look for her prodigal master.
Otkharev says that they should talk to Dr. Heightmeyer about Atlantis and the very idea of getting the expedition shrink to try therapy on the city... has stopped sounding quite so much like a joke as the weeks go by. Those with the gene talk of Atlantis being both jealous and elusive, hard to reach out to and harder still to disentangle from. Those who have had the gene artificially induced by therapy say she runs hot and cold, either ignoring them completely or letting them do more than they could before. It would be entertaining in a surreal way if it were not making a hash of daily life.
There are constant summonings of the technology-team-on-call because devices that have been working fine since someone with the gene initialized them almost two years ago are suddenly not working at all for anyone without the gene. Dr. Weir has gotten both locked in and locked out of her office and so far the armory door has been prised open five times to free Marines trapped inside. The medical team is having the least awkward time of it because Beckett is usually right there to fix things, but there is nobody in the Chemistry unit with the gene and they are afraid to work with hazardous materials lest their protective measures suddenly conk out on them.
The stargate, of course, is working fine and those in the command-and-control unit say that they can almost hear a hum of anticipation at each incoming wormhole, as if Atlantis is hoping that this time it will be Sheppard stepping through. It never is and Radek knows that Atlantis sulks each time because he has timed outages to offworld activation of the stargate. Caughlin and Verniere, the two who split what were once Peter Grodin's duties, have taken to trying to reason aloud with Atlantis. They tell her, in English, French, and Ancient, that each team is bringing back information that may help them find the missing team. Unsurprisingly, it does not seem to work.
Radek, who has no evidence except a gut instinct and a Bohemian soul, tells Dr. Weir one day that he does not think that Atlantis would go so far as to let herself get destroyed. She is being perverse and coy, true, but not suicidal. Nothing she has done to herself is permanent. If the Wraith were to come, she would fight more ferociously than she ever has because if she is going so far to spurn suitors born of the Ancients, then she would refuse the Wraith with that much more determination. She does not want a new love and master; she wants Sheppard to return.
Until then Atlantis waits, like Penelope at her loom, picking apart her beautiful handiwork when nobody is looking and keeping faith when those around her would falter.