A humanoid Cylon is captured in the fleet, a copy of the Leoben model, who claims that he has planted a nuclear bomb in the Fleet before he was captured. Starbuck is tasked with interrogating him, which soon becomes a battle of wills as Starbuck has her marines to torture the Cylon to try to break him.

The group on Caprica is under fire by the Cylons, but suddenly they stop. With only one ship's votes to be counted, Roslin is way behind in the elections.

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.

When a group of ill Cylons from the infected Basestar is brought to Galactica, Lee discovers a way to solve the Cylon problem forever - by destroying the whole Cylon race. Meanwhile, D'anna's acts to discover if Baltar is reliable will forge an unusual relationship.

The crew of Galactica makes a stop at the barren Algae planet.

The Cylons descend upon the re-supply mission as the Chief races to decipher the markings in the temple believed to hold The Eye of Jupiter, a sacred icon that is believed to contain a map to Earth.

The Admiral is forced to make the decision of whether to ground Kara Thrace when she begins to show signs of an oncoming nervous breakdown.

Starbuck (Katee Sackhoff) and Laura Roslin (Mary McDonnell) face off with a gun between them, Lee Adama (Jamie Bamber) says goodbye to the Galactica, violent conflict breaks out between the seven models aboard Cylon Basestar, and Gaius Baltar (James Callis) is directly pulled into the "Final Five" situation.

When a Heavy-Raider manned by Leoben Conoy docks aboard the Demetrius, confrontations form between the crew over the possibility of a truce with Cylon rebels, while Starbuck puts her trust in an old enemy.

A vicious injury ends the mutiny attempt aboard the Demetrius, Kara leads her crew to the Cylon rebel's Basestar, and Roslin begins to understand Gaius Baltar's appeal to his followers. Meanwhile, Anders attempts to secretly find answers to his purpose as a member of the Final Five.

A shaky alliance between the Colonial Fleet and Cylon rebels is put to the test when the two groups combine efforts to take out a Cylon "Resurrection Hub". Meanwhile, Athena loses control when Hera becomes unnaturally drawn to Natalie.

The Hybrid keeps jumping the basestar, and Roslin has visions. The three, D'Anna, is un-boxed. Humans and Cylons engage in a battle to destroy the Resurrection Hub. Baltar is badly wounded and Roslin has to decide whether or not to help him.

D'Anna demands that the four Cylons in the fleet be sent to the basestar. Only Tory goes, while the remaining three are suddenly drawn to Kara's Viper by the music. The route to Earth is finally found.

Scouting the planet reveals that there is no life except plants. The destruction occurred about 2,000 years earlier. Among the ruins, skeletons and wrecks of a different kind of Centurions are found. But closer examination of the skeletons reveals they are Cylon! Could the 13th Tribe really have been all Cylons? Chief Tyrol, Colonel Tigh, Sam Anders and Tory remember living on the planet and dying there. How did they get to the colonies? Starbuck finds a piece of her Viper, and despite Leoben's warnings, starts to look for the cockpit... Roslin loses her faith in the Scrolls of Pythia. Apollo and Dualla seem to get back together, but he needs to figure out what to tell to the people of the Fleet... A tragedy prompts Adama to confront Saul.

Roslin is on board a raptor en route to the Rebel Cylon Base Star, but Gaeta has ordered to engage and destroy it. The marines have used a stun grenade on Adama and Tigh. Roslin manages to get a wireless transmission out for everyone to hear and learn what Gaeta has done. She and the others barely make it to the Base Star, where she convinces Tory and the other Cylons to use the Fleet as a cover in order to prevent Gaeta from attacking it. She also believes that Adama will be able to save the rest of the Final Four. Temporarily safe, the Rebel Cylons start voting on whether they should just jump away and count their losses. Adama is brought before Gaeta and Tigh is thrown to the brig with Caprica Six, Anders, Athena, Helo and their child Hera. Zarek comes aboard Galactica on Colonial One with the Quorum. At Gaeta's insisting, Zarek agrees to put Adama on trial for treason, with Romo Lampkin assigned as his defence lawyer. There's just one problem: The Quorum refuses to recognize Zarek's authority. However, Zarek is hell-bent on following his "The truth is told by those left standing" maxim. Only Tyrol, who's alone, and Lee, whose with Starbuck, are Galactica's last hope.

As conflicts reach a climax, Cylons and humans face a stark choice.

A humanoid Cylon is captured in the fleet, a copy of the Leoben model, who claims that he has planted a nuclear bomb in the Fleet before he was captured. Starbuck is tasked with interrogating him, which soon becomes a battle of wills as Starbuck has her marines to torture the Cylon to try to break him.

The Admiral is forced to make the decision of whether to ground Kara Thrace when she begins to show signs of an oncoming nervous breakdown.

When a Heavy-Raider manned by Leoben Conoy docks aboard the Demetrius, confrontations form between the crew over the possibility of a truce with Cylon rebels, while Starbuck puts her trust in an old enemy.

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.

Roslin is on board a raptor en route to the Rebel Cylon Base Star, but Gaeta has ordered to engage and destroy it. The marines have used a stun grenade on Adama and Tigh. Roslin manages to get a wireless transmission out for everyone to hear and learn what Gaeta has done. She and the others barely make it to the Base Star, where she convinces Tory and the other Cylons to use the Fleet as a cover in order to prevent Gaeta from attacking it. She also believes that Adama will be able to save the rest of the Final Four. Temporarily safe, the Rebel Cylons start voting on whether they should just jump away and count their losses. Adama is brought before Gaeta and Tigh is thrown to the brig with Caprica Six, Anders, Athena, Helo and their child Hera. Zarek comes aboard Galactica on Colonial One with the Quorum. At Gaeta's insisting, Zarek agrees to put Adama on trial for treason, with Romo Lampkin assigned as his defence lawyer. There's just one problem: The Quorum refuses to recognize Zarek's authority. However, Zarek is hell-bent on following his "The truth is told by those left standing" maxim. Only Tyrol, who's alone, and Lee, whose with Starbuck, are Galactica's last hope.

Scouting the planet reveals that there is no life except plants. The destruction occurred about 2,000 years earlier. Among the ruins, skeletons and wrecks of a different kind of Centurions are found. But closer examination of the skeletons reveals they are Cylon! Could the 13th Tribe really have been all Cylons? Chief Tyrol, Colonel Tigh, Sam Anders and Tory remember living on the planet and dying there. How did they get to the colonies? Starbuck finds a piece of her Viper, and despite Leoben's warnings, starts to look for the cockpit... Roslin loses her faith in the Scrolls of Pythia. Apollo and Dualla seem to get back together, but he needs to figure out what to tell to the people of the Fleet... A tragedy prompts Adama to confront Saul.

D'Anna demands that the four Cylons in the fleet be sent to the basestar. Only Tory goes, while the remaining three are suddenly drawn to Kara's Viper by the music. The route to Earth is finally found.

The Hybrid keeps jumping the basestar, and Roslin has visions. The three, D'Anna, is un-boxed. Humans and Cylons engage in a battle to destroy the Resurrection Hub. Baltar is badly wounded and Roslin has to decide whether or not to help him.

A shaky alliance between the Colonial Fleet and Cylon rebels is put to the test when the two groups combine efforts to take out a Cylon "Resurrection Hub". Meanwhile, Athena loses control when Hera becomes unnaturally drawn to Natalie.

A vicious injury ends the mutiny attempt aboard the Demetrius, Kara leads her crew to the Cylon rebel's Basestar, and Roslin begins to understand Gaius Baltar's appeal to his followers. Meanwhile, Anders attempts to secretly find answers to his purpose as a member of the Final Five.