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.

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.

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.

Starbuck, Helo and Boomer bring back the Arrow of Apollo, but Boomer doesn't seem welcome. Commander Adama wants to keep the fleet divided and appoints a new CAG.

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.

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.

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.

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.