http://lostpedia.wikia.com/wiki/The_Incident_Room
This would also explain a lot from the previous seasons... when Sayid and Jack are beneath the Swan, checking things out... he says that the last time he saw anything like that... was Chernobyl... the atom bomb, coupled with the reactor that was used in harnessing the electromagnetic anomaly, needed to be closed off, and the station was instead re-converted into what it was in Season 2...
This may also be close to the time when The Others take control of Dharma (I personally think that is what happens... they leak inside and set things up - which would explain why The Others so easily got into the village during "The Purge"... Benjamin Linus was older, and he had been saved from death. He was somewhat in control there.
The next season may deffinetly be about The Others, and it may tie up a lot of questions about the island itself, and how the people play they're roles, but I don't think some of the "mysterious" questions will ever be answered. Because that is what the island works off of, mystery... we are supposed to trust it just as John Locke trusts it - because that man has his s*** together!
I'm eagerly awaiting the next episode... "The Incident Pts. 1 & 2" (Yes! A two-houre finale!)