The Galactica and the other remaining ships - with about 50,000 people aboard them all - are being pursued by the Cylons. They are forced to jump into hyper space every 33 minutes. Somehow, the Cylons know where they are going and appear exactly 33 minutes after the Galactica arrives. The crew hasn't slept for over 130 hours now and everyone is exhausted. They rejoice when they finally make a jump and the Cylons fail to appear at the 33 minute mark. They are also prone to make mistakes and realize they've left behind a ship, the Olympic Carrier, with 1300 passengers aboard. When the ship rejoins the fleet a few hours later, the Cylons again arrive 33 minutes later leading Adama to conclude that there are Cylon spies on board. President Roslin now faces a major decision. The identity of the the Cylon aboard the Galactica is revealed.

President Roslin arrives on Galactica as Boomer's Cylon side asserts itself, forcing her to sabotage Galactica's water supply against her will. A series of explosions leads to the loss of 60% of the water reserves and Commander Adama is compelled to introduce rationing and begin a search of nearby planetary systems for any H20 deposits.

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.

After Baltar has an argument with the vision of Number Six he sees in his head, a physical copy of Cylon model Number Six shows up in Galactica's CIC claiming to be a woman named Shelley Godfrey who has evidence that proves that Baltar has betrayed humanity...except that she's trying to frame him for an act of pre-attack sabotage.

The fleet is running out of tylium fuel and will soon not have enough to keep running from the Cylons, when they find an asteroid with several years worth of tylium ore...unfortunately, the Cylons have already built a mining base on it.

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.

Galactica stumbles upon Kobol, the long-lost home world of humanity that the 13 Tribes came from, which legend says holds the only clues to the location of Earth. Roslin convinces Starbuck to steal the captured Cylon raider and return to Cylon-occupied Caprica with it to retrieve a religious artifact that will unlock the secrets on Kobol.

Infuriated that Roslin usurped his command by ordering Starbuck to steal the captured Raider, Adama decides that his only option is to storm Colonial One with marines and terminate her presidency. Starbuck reaches Caprica and finds the Arrow of Apollo in a museum, but she has to go through a copy of Number Six to get it.

As the premiere for the second season unfolds, Adama lay dying leaving Tigh in command. Lee and Roslin have been sent to the brig. An emergency jump goes wrong leaving the Galactica alone in space without the fleet.

A Cylon virus is interfering with Galactica's power supply, while Cylon centurions are heading for crucial systems. Somehow they must be stopped.

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.

While Tyrol decides to start building a new fighter, the Cylon virus is rearing its ugly head again. Boomer says it means a large Cylon attack is imminent.

Gallactica meets Pegasus, and Adama's command is threatened when the captain of Pegasus outranks him. A joyous celebration turns sour at some of the secrets emerging out of the differences of the two crews, and Baltar meets a familiar Cylon prisoner aboard Pegasus.

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.

President Roslin, who is about to die, believes Sharon's baby is dangerous and orders it must die. Meanwhile, a terrorist group inside the fleet starts to ask for a peace negotiation with the cylons.

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.

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.

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.

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.

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 Chief and his wife get trapped in an airlock on a routine maintenance job, while the Admiral copes with his wedding anniversary and the memories of his ex-wife.

When the head of the fuel production plant holds the fleet hostage by providing unsafe fuel, he's arrested for treason, which results in the Chief sent to the ship and held responsible for getting the plant back up and running.

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.

Coincidences creates new alliances aboard Galactica.

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.

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.

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

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 Chief and his wife get trapped in an airlock on a routine maintenance job, while the Admiral copes with his wedding anniversary and the memories of his ex-wife.

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.

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.

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.

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

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.

A Cylon virus is interfering with Galactica's power supply, while Cylon centurions are heading for crucial systems. Somehow they must be stopped.

When the head of the fuel production plant holds the fleet hostage by providing unsafe fuel, he's arrested for treason, which results in the Chief sent to the ship and held responsible for getting the plant back up and running.

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.