The Cylons have now been in control of New Caprica for over four months. Gaius Baltar is under their collective thumbs and essentially follows their orders. There is a resistance who set off bombs and do their best to disrupt Cylon activity. Col. Tigh is in prison and despite extensive torture, including the loss of an eye, has told them nothing. His wife Ellen will do anything to secure his release and is soon in a sexual relationship with one of the Cylons, John Cavil. There are mixed feelings among the survivors. Some feel the random acts of violence against their captors serves no useful purpose while others feel it is their duty to resist. Kara Thrace, Starbuck, is being kept prisoner in an apartment of sorts by Leoben Conoy. She too resists but every time she kills him, he is simply re-generated and reappears insisting he will continue to do so until he tells her she loves him. Back on Galactica, Admiral Adama takes his son Lee, Commander of the Battlestar Pegasus, to task for going soft.

As a result of the most recent suicide bombings, some of the Cylons are now arguing that they need to retaliate. Laura Roslin, among others, is in custody and Gaius Baltar tries to get her to cooperate. Tigh however absolutely refuses to stop the suicide bombings. Nighttime raids also leads to Cally's arrest but they leave her baby alone. Sharon Valerii sees what she can do about it. John Cavil meanwhile tells Ellen Tigh she is to provide the date and location of the next meeting of the resistance commanders. Leoben Conoy is still holding Starbuck prisoner but introduces her to her daughter, Kacey, produced from eggs they harvested from her when she was on the Farm. On Galactica, Admiral Adama begins to plan for a massive rescue of everyone on New Caprica. He realizes they will have to obtain the launch keys for all of the ships on the planet's surface. The best way of infiltrating the Cylons is with another Cylon so Adama commissions Sharon Agathon as an officer.

The secret source in the administration has provided Tyrol with a list of all humans scheduled for extermination. Tyrol's wife Cally is on the list and he sets off to rescue her. Sharon Agathon has made it safely to the planet but they are ambushed by Cylons lying in wait. They realize they were betrayed and Anders finds damning evidence that points to the identity of the traitor. D'Anna Biers has been having strange dreams of late and an oracle tells her that the child Hera is alive and she will hold her in her arms. Roslin meanwhile assigns a squad of men to protect the child at all costs. The Admiral sends the Pegasus away with the few remaining civilian ships to continue the search for Earth.

The attack to rescue everyone on New Caprica begins. The Galactica encounters four rather than the expected two Cylon Basestars. The end appears in sight but they get help from a welcome but unexpected source. On the planet below, Tyrol and Anders lead the attack to free everyone from the prison. Anders finds Starbuck but she won't leave without Kacey. Her successful return to the Galactica results in mixed emotions. Colonel Tigh must decide what to do about his wife Ellen after she admits to giving the rendezvous coordinates to the Cylons. Hera doesn't make it off the planet.

Baltar learns from Caprica Six of their ability to project themselves and imagine different surroundings which leads him to wonder if he too is a Cylon. He has told the Cylons what he knows about the location of Earth and they dispatch a Basestar to investigate. In the end, the survey ship is infected with a virus killing everyone aboard. Aboard the Galactica, Lt. Gaeta has been reviewing Baltar's work in deciphering the map they recovered on Kobol. He too thinks he knows what it all means. Of greater concern however is the wedge between those who stayed with the fleet and those who were on the ground fighting the Cylons. Starbuck and Colonel Tigh in particular are quite vocal in complaining about those who stayed behind and it's left to Admiral Adama to lay down the law.