The Sickness by EmilyG

The Others clearly fear the Infection, but I don't believe for a second that they truly understand what "it" is. So here's my theory:

I think "the infection" ties into the alt-reality: specifically, the 'infected' aren't being subsumed by Smokey---they're becoming integrated with their selves from the alt-verse. That's why it seems like they've gone crazy---their actions make no sense from the perspective of "our" timeline, but they may in fact make perfect sense if these people are operating in the context of their experiences in the alternate universe.

Maybe Danielle Rousseau went crazy in the alt-verse and tried to kill her teammates for no reason, and when her team was 'infected', they 'remembered' that and turned on her in the original timeline? To us, we saw Robert trying to kill the mother of his child; to him, he was acting preemptively to save himself from what he remembered as Danielle's madness. (Hell, maybe Danielle was the one "infected" in the alt-verse, and she went homicidal based on 'memories' of the original timeline. It would be nicely ironic.) Also, remember, we've only seen glimpses of the alt-verse through 2004: the 'original' timeline is still in 2007, so there's a three year gap between original and alt that we haven't experienced yet. Maybe something happened to alt-Claire in this three-year gap that accounts for her new badass skills (and the personality shift that Dogen referenced)?

And another thought: the timeline we know always had the Losties end up in the 70s (because of the picture that "Christian" showed Sun and Frank). It's been hinted that DHARMA had some inkling about "the sickness"---the vaccinations of new recruits, the "quarantine" signs everywhere (can't be a reference to the gassing of the Purge---the Purge was over too quickly for signs to be made). Since Season 5 ended, I've wondered how DHARMA interpreted the events leading up to The Incident: one day, all of a sudden, the heretofore loyal Head of Security, his dependable mechanic/doctor girlfriend, and most of the Security Team suddenly start "going insane." Lafleur knocks out and ties up his subordinate Phil, and participates in the kidnapping of a child. The gentle physicist Daniel Faraday shoots Radzinsky. Jin starts running around screaming nonsense about a plane landing on the Island. A "Hostile," who for some reason is handcuffed, wanders into DHARMA territory, won't explain why! , and then later tells a story about time travel. The new recruits, who CANNOT have ever met Lafleur et al before, are acting just as bizarrely. From DHARMA's perspective, LaFleur, Juliet, etc. can't be Hostiles---first, because Juliet clearly has advanced medical training (and DHARMA thought the Hostiles were a bunch of psychotic savages), and second, because if LaFleur was a Hostile, he'd have helped the Hostiles destroy DHARMA years ago.

So maybe DHARMA thought the 77 Losties were, in fact, "infected," and that's what instigated their bizarre behavior. Just as the behavior of James/Juliet and the rest would seem insane to an 'outsider', so too does the behavior of the 'infected' seem insane to those who don't really understand where these people's motivations are coming from.

If Smokey/MIB represents free will (with his 'I will release you' schtick), maybe this is how he does it: he allows people to 'remember' a world where they made different choices, and this is how they have the ability to truly make informed choices in their current reality, and thereby change their fates. So what Dogen told Jack was true, from a certain pov: the infection comes from darkness (the Man in Black) and it transforms people; it's just that Dogen didn't understand he wasn't truly giving Jack the whole story.