Adama and Cain find common ground when Starbuck returns with footage of the Cylon ship. Roslin negotiates a temporary truce, while Starbuck plans an attack.

Galactica and Pegasus are preparing for the assault on the Cylon Resurrection ship. While Starbuck discusses Adama's plan to kill Cain with Apollo, Colonel Fisk stops Pegasus' crew members beating up Helo and Tyrol. He dispatches his marines on Galactica to execute Cain's plan to kill Adama. Apollo seems to dislike his father's plan and hears him out before he sets off in the blackbird to destroy the FTL-drive of the Resurrection ship. It goes wrong for him. Meanwhile Dr. Baltar is trying to take care of the Number Six on Pegasus. He seems to have feelings for her, much to the dismay of the Number Six in his head.

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.

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 Colonial fleet makes a harrowing journey. Kat plays a vital role in the success or failure of the passage.

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.

Coincidences creates new alliances aboard Galactica.

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.

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.

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.

Ellen and Boomer travel to the Galactica. Saul is entranced at the sight of his wife while Adama puts Boomer in the brig. Ellen is not so pleased when she learns that Caprica Six is pregnant by Saul. Her interference and jealousy leads Six to have a miscarriage. Sam Anders survived the operation but now seems to be brain dead. Ellen is disappointed that the Final Five cannot be completely reunited. By majority vote, the Five agree that they will go off on their own, leaving the Colonial Fleet behind. Adama has agreed to have the cracks in the Galactica's hull repaired using a Cylon living resin.

Kara meets a pianist who reminds her of her father. She tries to play a melody she remembers from her childhood, and a drawing made by Hera helps her. Meanwhile, Boomer is to be tried for treason. Tyrol takes her side, and helps her escape.

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.