Sharon informs Adama that the Galatica has been infected with a computer virus that is tampering with the basic ship functions and is scanning them for weaknesses. All this is preparation for a major assault by the Cylon Raiders. So with the clock ticking

A crazed Cylon Raider attacks the Colonial fleet in a series of hit-and-run attacks. Overworked Viper pilots must defend a mining operation from this Raider that they nickname "Scar."

The Colonial fleet faces starvation when the food-processing machines are contaminated. Kat plays a vital role in the success or failure of the "Passage" through space.

Kara continues to have dreams about Leoben Conoy and the mandala she painted at her old apartment on Caprica. While on patrol in her Viper, she encounters a Cylon Heavy Raider. When Tyrol cannot verify Kara's claim that the Cylon ship struck the Viper, Admiral Adama and Lee become concerned about her mental stability.

Kara Thrace seeks her own path in the search for Earth while the Cylons face the threat of sentient Centurions. A member of Galactica's crew learns a dark secret about a loved one.

The dying President Roslin and the aggressive Viper pilot Kara Thrace try to accept the new terms of the relationship with the Cylons.

Kara struggles with the foreboding prediction of the Cylon Hybrid, while Adama and the Colonial fleet face despair over their shocking discovery.

Kara feels lost while she struggles to cope with Sam's continued coma, meanwhile Boomer faces charges of treason from the Cylons onboard the base ship who blame her for voting against her model during the civil war causing the deaths of thousands of Cylons.