The third season begins with freedom fighters on New Caprica, which has been under Cylon Rule for half a year. Baltar had been voted President and is basically an in-name only ruler. Gaita is his right hand man, though he's secretly working for the Resistance. The two Battlestars are nowhere to be seen and everyone feels like they have to fend for themselves. Former President Laura Roslin is back to being a school teacher, Chief is married to Callie and has a young son. Colonel Tigh is in prison and has lost an eye, though he refuses to tell the Cylons anything. His wife, Ellen, is determined to get him freed and gets in a sexual relationship with John Cavil, who is one of the Cylons. Kara is being kept prisoner in an apartment by Cylon Leoben, who says that he loves her. She's convinced that the child he shows up with is indeed hers, from that time she was taken prisoner on Caprica in Season Two. We also learn certain key things about Kara, such as how she was physically abused by her mother. By the fourth episode the Battlestars return and the majority of the people manage to escape from the Cylons, though there's a huge cost. Their trek for Earth continues.
The majority of the episodes deal with the repercussions of having fought against or supported the Cylons on New Caprica. Some surprising decisions are made, especially in regard to Laura Roslin. And Baltar is thrown in prison and put on trial.
Starbuck may have a much larger role in humanity's destiny than she realized when it's revealed that the symbol they find on a four thousand year old temple on a planet is the same painting she did every since she was a child. There must be a connection but what that is is not answered until the very end of the Fourth Season. Her behavior becomes more and more erratic, like she's having a nervous breakdown.At the end of the season she pursues a Cylon Raider into the clouds on a gas planet and Apollo sees her ship explode. Yet she returns in the last episode in her Viper, saying that she's found Earth and she's back to lead them there. This is unexpected, to say the least.
The biggest thing that happens is that four of the five "Final Five Cylons" are revealed, which will change everything.