Ok this is from memory and may be some gaps.
Gaeta was injured in Big battle with bunch of cylons.
Other cylons however rebelled against the main group and after a short civil war between the rival cylons joined with Galactica in search of earth. This happened right before the season break.
Kara also went a bit bonkers obsessing about having visited earth. Hence the weirdness over finding her own body on earth.
Personally i think we will eventually find that we are all cylons and that the mice run the planet. Or perhaps I'm getting my sci-fi mixed up.
Hope this helps