Everything is much more dire in this second season. It begins with Commander Adama being shot by the Cylon Sharon. Tigh takes over command of the Fleet but he does a crappy job, goaded on by his alcoholic wife Helen. President Roslin is in the brig because she disagreed with Adama at the end of season one. And Starbuck is back on Caprica to retrieve the arrow of Apollo which will lead them to Earth. There, she encounters Helo and another Sharon Valeri. While he's been trying to survive on Caprica Helo has fallen in love with this woman he thought was his friend--and she becomes pregant, a first ever between human and Cylon.
Starbuck also comes across other survivors, players from a Pyramid Team (like Rugby) and she falls for their leader. But she's shot and wakes up in a hospital. However, she's suspicious that the doctor is really a Cylon and that they want her for some nefarious purpose. She is correct. They have other human females captive and are using them for breeding experiments with Cylons. Eventually she, Helo and this other Sharon make their way back to the fleet, though the Cylon is immediately imprisoned. And two more human-looking Cylon's are revealed, Deana (Lucy Lawless) and Cavell (Dean Stockwell).
The season ends on an unexpected note, with Baltar being elected president and deciding to settle on the planet which they call New Caprica. It then skips a year and we see that 90% of the people are now living on the surface of the planet. The fleet, with a skeleton crew, is in orbit. Kara is married to Anders, who is sick with pneumonia and when she calls Apollo, who is up in Pegasus, for some antibiotics, we see he's very angry and fat. In the last scene we see the Cylons invading the planet and the mechanical troops marching down the middle of the makeshift city, like a Nazi parade in WWII.
I didn't quite like this as much as the first season but it does set up the rest of the events for the next two years.