Deciding to use the thousand prisoners on a prison transport ship to mine the ice on the planet they've found, Galactica's plans are upset when a political prisoner onboard leads an uprising, taking hostages. He questions the legitimacy of Roslin's government and demands free elections to be held in the fleet.

President Roslin has rebuilt a new Quorum of Twelve, the legislative branch of the government, but terrorist leader/political dissident Tom Zarek is elected as a member, and immediately motions that the Quorum vote to appoint a new Vice President, and runs for the office.

Tigh has problems with the responsibility of being a leader, president Roslin loses control without chamalla. The Kobol team discovers a Cylon battery.

Tigh's decision to impose martial law is protested in the fleet as well as on Galactica. On Caprica, Helo and Starbuck meet other humans.

Starbuck finds herself wounded in a hospital on Caprica where she is suspicious about her doctor. President Roslin makes an appeal to the fleet to follow her to Kobol.

Starbuck, Helo and Boomer bring back the Arrow of Apollo, but Boomer doesn't seem welcome. Commander Adama wants to keep the fleet divided and appoints a new CAG.

While Commander Adama tries to join Roslin's team on Kobol, Dr. Baltar's Number Six tells him he's crazy.

Apollo investigates the murder of one of the crew and falls for a young prostitute, whom he vows to save from the rogue ship dealing with the Black Market. As well as confronting the bad guys, Apollo has to confront some past mistakes.

Two of Pegasus' raptors go missing after a suspicious distress call. President Roslin must make a decision on abortion that could hurt her political career.

While Dr. Baltar is behind in the polls for the election and tries desperately to turn things around, Starbuck is planning a mission to rescue Anders from Caprica.

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.

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.

Now safely back in the fleet, those who managed to escape from New Caprica are seeking revenge against those they believe collaborated with the Cylons. Six of them, including Chief Tyrol and Col. Tigh, have formed the Circle and are acting as judge, jury and executioner. Those found guilty are blown out of an airlock. Lee Adama has noted that in the three days since everyone was reunited, 13 people have simply disappeared without a trace. The morale aboard the Galactica is not good with perceived collaborators being shunned by the others. Among those in that situation is Felix Gaeta who, as Gaius Baltar's Chief of Staff, is high on the Circle's list. As for Baltar is now being kept aboard a Cylon Basestar and his captors are deciding his fate as well.

When a group of refugees board Galactica with a curable illness, it becomes very mysterious when they begin to die after taking the injection they do not believe in.

The aftermath of a coup among the Cylons leads to further violence, Lee finds himself facing off against Roslin during his first meeting with the Quorum of Twelve as the new representative of Caprica, and Cally discovers the horrible truth about her husband Galen Tyrol. Meanwhile, Starbuck aimlessly searches for Earth with Anders and other Galactica officers.

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.

President Roslin's abduction by the Cylon Hybrid triggers a bitter power struggle within the Colonial Fleet.

Adama considers Saul and Tyrol's suggestion that the Fleet should integrate Cylon jump technology since it will triple the distance they will be able to cover before they run out of fuel. But the Cylon's condition is that they will be allowed to join the Fleet, for safety against Cavil, who's still out there. Ultimately, the decision is up to President Roslin, but Zarek calls the Quorum and gets them to carry the motion that no Cylon be allowed aboard any Colonial vessel unless permitted by the ship's captain. Tyrol learns from Dr. Cottle that Cally had their child tested and the results indicated that Tyrol is not the father - therefore the child is fully human. Roslin starts her climb up from the depths of despair she had fallen to soon after the Fleet found Earth.

The Fleet refuses to cooperate with Cylon engineers and Adama decides to put an end to it. He sends the Quorum a message stating that unless they wish to join Zarek in the cell, they get their people in line. However, Gaeta has already freed Zarek with the help of other would-be-revolutionists. They allow Zarek to leave Galactica on a raptor. He lands on Colonial One and enters a gathering of the Quorum. Meanwhile, Anders gets ambushed and captured. At the CIC, Gaeta cleverly manipulates everyone else until the time is at hand for the revolution to begin.

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.

President Roslin has rebuilt a new Quorum of Twelve, the legislative branch of the government, but terrorist leader/political dissident Tom Zarek is elected as a member, and immediately motions that the Quorum vote to appoint a new Vice President, and runs for the office.

Deciding to use the thousand prisoners on a prison transport ship to mine the ice on the planet they've found, Galactica's plans are upset when a political prisoner onboard leads an uprising, taking hostages. He questions the legitimacy of Roslin's government and demands free elections to be held in the fleet.

Adama considers Saul and Tyrol's suggestion that the Fleet should integrate Cylon jump technology since it will triple the distance they will be able to cover before they run out of fuel. But the Cylon's condition is that they will be allowed to join the Fleet, for safety against Cavil, who's still out there. Ultimately, the decision is up to President Roslin, but Zarek calls the Quorum and gets them to carry the motion that no Cylon be allowed aboard any Colonial vessel unless permitted by the ship's captain. Tyrol learns from Dr. Cottle that Cally had their child tested and the results indicated that Tyrol is not the father - therefore the child is fully human. Roslin starts her climb up from the depths of despair she had fallen to soon after the Fleet found Earth.

President Roslin's abduction by the Cylon Hybrid triggers a bitter power struggle within the Colonial Fleet.

Now safely back in the fleet, those who managed to escape from New Caprica are seeking revenge against those they believe collaborated with the Cylons. Six of them, including Chief Tyrol and Col. Tigh, have formed the Circle and are acting as judge, jury and executioner. Those found guilty are blown out of an airlock. Lee Adama has noted that in the three days since everyone was reunited, 13 people have simply disappeared without a trace. The morale aboard the Galactica is not good with perceived collaborators being shunned by the others. Among those in that situation is Felix Gaeta who, as Gaius Baltar's Chief of Staff, is high on the Circle's list. As for Baltar is now being kept aboard a Cylon Basestar and his captors are deciding his fate as well.