The Cylons have attacked the humans, and they're hitting them hard. They have managed to take down most of the human technology, but the Ghost squadron doesn't use the vulnerable software that the other human tech uses, and have managed to remain active. So, with the technology secure, they only need to worry about insurrection, a shortage of manpower, a lack of sufficient numbers to put up a decent fight, an inability to resupply, and Cylon infiltrators they don't even know they should watch for.