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.

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 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.

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.

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.

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.