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.

A humanoid Cylon straps himself with explosives and commits a suicide bombing in a crowded hallway on Galactica. Roslin and Adama are forced to publicly reveal that the Cylons now have models that look like humans, and a wave of paranoia spreads over the fleet as everyone starts being suspected of being a Cylon.

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.

After the interrogated Cylon gave Roslin the idea that Adama might be a Cylon, Roslin becomes suspicious of him. Unexpectedly, Colonel Tigh's estranged wife Ellen turns up alive in the fleet, apparently miraculously, raising the possibility that she might be a Cylon.

Journalist D'Anna Biers is making an item on the Gideon incident, when she's asked by Adama and Roslin to film daily life on Galactica.

The Cylon baby is finally born, leading to some political decisions being made. Meanwhile, the Cylons on Caprica contemplate life and humans when they meet up with a certain human from a previous episode. This story explores the Cylon world.

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.

A figure from Adama's past returns to haunt him. His return raises questions about why the Cylons launched their initial attack against the Twelve Colonies.

Coincidences creates new alliances aboard Galactica.

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.

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.

The Colony is located sitting on the edge of a black hole with only one point of entry in what is a very large debris field. Knowing that the Galactica has reached the end of the line, Admiral Adama asks for volunteers to mount a raid on the Cylon base, realizing it may be the ship's last jump. In flashbacks prior to the Cylon invasion, key moments in the lives of several of the crew are presented. These include include the first time Kara Thrace and Lee Adama meet; Admiral Adama's struggle with his decision to retire from the colonial fleet; Gaius Baltar's relationship with his father and his developing relationship with Caprica Six; and Sam Anders discussing the motivation behind his professional sports career.

A stripped down Galactica attacks the Cylon's Colony ship in the hopes of rescuing Hera. The meaning of the shared dream in the Opera House on Kobol is revealed. Sam Anders is moved in his Hybrid tank to the CIC in the hopes that he will be able to assist the combatants. Their mission complete, Admiral Adama orders Starbuck to pick a destination - any destination - to which the ship can jump to get out of there. With that, the meaning of the tune and the musical notes are explained. Having successfully jumped, the old Galactica has truly reached the end of it's life. A planet capable of sustaining life is found and Lee Adama makes a radical proposal for the future of humankind. In a flash forward far into the future, Hera's importance to the human race is revealed.

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