Rousseau seemed to be strangely uninterested in that building and its occupant. Almost as if she already knew who and what was in there...
I am turning around two different theories in my mind.
One--Danielle is in fact the last surviving member of the Dharma Initiative. That was the group of scientists that she was a part of. She was the only one to survive "the purge" and possibly she was the one who made the deal to be left alone if she stayed on her side of the line (which might literally be that cable running to the beach). Possibly the price of her survival was to give up her daughter and she agreed to it, and what she did has driven her mad over the years. Kids seem to be a hot commodity on the island--maybe the Others struggle with infertility, hence the need for a reproductive specialist like Juliet and the propensity to kidnap children to continue their survival. Anyway, how can Rousseau have been scouting around the island for 16 years and claim to have never seen one of the Others? I think she was lying about that. When she caught Ben/Henry last season she seemed pretty sure who he was and warned that everything he said would be a lie. She's obviously a little unstable, but it seems that she isn't telling the whole truth about her history on the island, crazy or not.
My next theory is that she herself was once a part of the Others but was expelled for whatever reason. Maybe she was recruited from the mainland like Juliet, and Ben has a thing for bringing new ladies to the island every now and then for a little loving. Maybe a big twist would be to discover that Alex really is the daughter of Ben and Rousseau. Maybe Ben got her pregnant and shortly after the baby was born something caused a falling out between them. So they kept her child, stuck her in Room 23 for a little mind melting, and then released her now crazy self onto the main island. I wouldn't be surprised at all if we get a big reveal this season and discover that Rousseau has the same branding/scar that Juliet received as her punishment. Maybe her capturing and delivering Ben to Jack and Co. was an attempt to start the wheels turning that are now in motion--exposure to the Others and assistance in the recovery of her daughter.
And I also wonder if the Flame hatch was the place where Danielle went to program the looped recording that Sayid discovered in season one. Either a background with Dharma or with the Others, post-purge, would have given her knowledge about the location and communications technology in that building. The upstairs computer that claimed the communications were dead could have been a decoy. Maybe there was actual working equipment downstairs. Now we'll never know.
Thanks, Locke!! Stop blowing up hatches!! We know you will do anything to keep from leaving the island, but don't hurt everybody else's chances...
