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i think he knew the station existed and what its purpose was... after all he used to work for Dharma, i think he knew about kelvin being down there, as my guess is he knew pushing the button was vital for the good of the island or whatever, and i think he would have known that kelvin was down there, either because kelvin had survived the purge being in the hatch or that kelvin was another dharma person who had been converted to the others. i dont think he knew about desmond though because he seemed surprised when he found out that sayid and jin and sun had a boat at the begining of season 3 when colleen told them

oh my god i think iv just realised what the sickness is (sorry to change the subject) but the swan doors had quarantene written on them, to stop people going outside, the purge that was carried out by the others seemed to invoolve some sort of killer gas, maybe the sickness was caused by the gas still being around for a while after the purge, but its affects were not as instant and killed people off slowly