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.

This is an episode about loss. Kat and Starbuck confront each other about their piloting skills and each vow to kill Scar (a Cylon spaceship) before the other.

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.

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.

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.

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.

A look at the events that took place during the year-long gap from the storyline in the Season Two finale. The story reveals the reasons for the rift between Kara ("Starbuck") and Lee ("Apollo").

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.

Baltar plays a game of cat and mouse with Adama and the President, thinking they will kill him once they've gotten out of him what they want to know. Lee deals with his feelings for Kara, while struggling to hang on to his marriage.

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.

Besides having to deal with the loss of Kara Thrace, the crew of the Galactica is also charged with the security surrounding the trial of Dr. Baltar and his defense attorney, who is replacing one lawyer that has already been killed.

Baltar goes on trial for his life, and it affects everyone from Lee on up to the president.

Coincidences creates new alliances aboard Galactica.

During a seemingly hopeless battle, Kara Thrace appears in a pristine Viper, claiming that she has been to Earth and can lead the Fleet there -- but the terminal Laura Roslin believes otherwise. Meanwhile, four of the so-called Final Five are forced to tackle the repercussions of their newfound nature, while Gaius Baltar discovers he has a commune of nubile female cultists who believe him to be an agent of the "one true God".

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.

Gaius Baltar causes intense unrest within the fleet when he begins to openly promote belief in the Cylon god. Colonel Tigh, Galen Tyrol, and Tory Foster argue over how far they should go to ensure their secret is not revealed.

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.

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.

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.

Eighteen months ago: Saul poisons Ellen, who then finds herself downloaded into a new body aboard a Cylon Base Star, with a single Centaurion keeping watch over her. After the initial shock, she has a revelation as she remembers things she had forgotten. Present Day: Dr. Cottle is operating on Anders, who has a bullet lodged in his brain. Anders starts to remember things he had forgotten. Eighteen months ago: Cavil comes to see Ellen, who calls him John, because that's his "real" name. Cavil says he hates that name. John was the first Cylon model *Ellen* created. She also created seven others. So, there are actually only *eight* Cylon models and the "Final Five" are actually copies of humans who lived 2,000 years earlier and, together, created Resurrection, which allowed them and the Cylons to download. Number Seven, Daniel, was a favorite of Ellen. Jealous, John sabotaged the process of using Resurrection on Daniel, making him unique. John and Ellen start a months-long philosophical and ethical argument on Cylon - human interaction. John says he started the genocide of humankind because his "forebears on the Centaurion side of the family were the slaves of humanity." And he wants justice for that. Present Day: Anders tells Starbuck that he has seen "everything" and needs Kara to get "the others" - Galen, Tory, Saul and Ellen to his bedside. Anders says he remembers everything and knows why they have come all the way to Earth... Adama reinstates Tyrol as a Chief of Engineering. Tyrol starts inspecting the damage Galactica has taken during their journey. But he is not prepared for what he finds and Adama is not prepared for what Tyrol suggests as a repair method.

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.

With Hera now likely in the hands of John Cavil, Admiral Adama sends out search teams to locate The Colony, the Cylon home world if you will, that Ellen Tigh says is the only place she imagines she could be. Adama reluctantly comes to the conclusion that the Galactica has reached the end of its days. He orders all repair activities halted and decides to strip the ship and share everything that is salvageable with the rest of the fleet. Starbuck meanwhile shares with Gaius Baltar what she found on the uninhabitable Earth. He subsequently - and quite publicly - proclaims her to be an angel.

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.

Eighteen months ago: Saul poisons Ellen, who then finds herself downloaded into a new body aboard a Cylon Base Star, with a single Centaurion keeping watch over her. After the initial shock, she has a revelation as she remembers things she had forgotten. Present Day: Dr. Cottle is operating on Anders, who has a bullet lodged in his brain. Anders starts to remember things he had forgotten. Eighteen months ago: Cavil comes to see Ellen, who calls him John, because that's his "real" name. Cavil says he hates that name. John was the first Cylon model *Ellen* created. She also created seven others. So, there are actually only *eight* Cylon models and the "Final Five" are actually copies of humans who lived 2,000 years earlier and, together, created Resurrection, which allowed them and the Cylons to download. Number Seven, Daniel, was a favorite of Ellen. Jealous, John sabotaged the process of using Resurrection on Daniel, making him unique. John and Ellen start a months-long philosophical and ethical argument on Cylon - human interaction. John says he started the genocide of humankind because his "forebears on the Centaurion side of the family were the slaves of humanity." And he wants justice for that. Present Day: Anders tells Starbuck that he has seen "everything" and needs Kara to get "the others" - Galen, Tory, Saul and Ellen to his bedside. Anders says he remembers everything and knows why they have come all the way to Earth... Adama reinstates Tyrol as a Chief of Engineering. Tyrol starts inspecting the damage Galactica has taken during their journey. But he is not prepared for what he finds and Adama is not prepared for what Tyrol suggests as a repair method.

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.

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

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.

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.

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.

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.

During a seemingly hopeless battle, Kara Thrace appears in a pristine Viper, claiming that she has been to Earth and can lead the Fleet there -- but the terminal Laura Roslin believes otherwise. Meanwhile, four of the so-called Final Five are forced to tackle the repercussions of their newfound nature, while Gaius Baltar discovers he has a commune of nubile female cultists who believe him to be an agent of the "one true God".

Besides having to deal with the loss of Kara Thrace, the crew of the Galactica is also charged with the security surrounding the trial of Dr. Baltar and his defense attorney, who is replacing one lawyer that has already been killed.