Explain please, thanks.
.. er.. and why are the cylons holding the humans in the first place when they said they were going to go away and leave them alone in series 2?
Almost the entire civilian fleet and most of the crews of the Pegasus and Galactica go planetside. A few years pass and some Cylon vessels passing through the area detect the nuclear signature of the bomb Six set off and investigate the cloud. They find New Caprica, basestars jump in, and the two Battlestars, undermanned and soft from their time off, retreat. The Cylons take over New Caprica.
And that roughly sums up the last few episodes of 2.5. The mini-series on the site covers things between the end of 2.5 and the start of 3.
I tried hunting it down in other places but never got anywhere with that, so I gave up trying.
That was a very satisfying episode. 
