When a new copy of Doral, a Cylon who had been previously exposed while serving as the Galactica's public-relations officer, sneaks aboard and blows himself up, killing three people, Commander Adama and President Roslin must finally make public the terrifying secret known only to a select few: Cylons now look like humans.

Tigh has to work with Lee to defeat a Cylon boarding party that threatens to take over Galactica and destroy the fleet.

Tigh imposes martial law and threatens to split the fleet as Lee works to free President Roslin and organize democratic resistance.

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

Tigh, Tyrol and Anders lead the Resistance on New Caprica to increasingly deadly attacks against the Cylons. Kara finds herself trapped in a new life with Leoben Conoy, and Duck makes a fateful decision. Meanwhile on Galactica, Adama struggles with the question of whether to return to New Caprica to mount a rescue attempt.

Adama plans to return to New Caprica and drop off a surprising person to act as a liaison between Galactica and the Resistance. Tigh's insistence on the use of suicide bombers and ever escalating violence stuns even the fellow leaders of the Resistance. Eventually, the suicide bombings cause the Cylon occupiers to crackdown on their human subjects.

Sharon helps the Resistance on New Caprica as Adama leads Galactica on a dangerous rescue operation. Tyrol races to save Cally from the execution squad. Meanwhile Anders uncovers treachery among the humans. Number Three meets the Oracle Selloi after having strange dreams about the temple.

Tigh must decide the fate of his wife Ellen after the assistance she rendered to the Cylons. Lee struggles with his assignment to protect the civilian fleet on its journey toward Earth while Adama returns to New Caprica with just the Galactica. The Resistance coordinates an attack on the Cylons just as Galactica arrives. As the Cylons begin to lose control, Number Three vows to put a final end to the New Caprican experiment.

Tyrol participates in the Circle, a secret tribunal on Galactica that tries and convicts in absentia those accused of collaborating with the Cylons during the Occupation. The death sentences--administered without the knowledge of Roslin or Adama--begin to weigh on Tyrol's conscience. Baltar faces a similar jury among the Cylons, who must decide whether he is allowed to stay with them.

Adama stages a boxing tournament on the Galactica to help the crew relax. The competitive atmosphere sets off a brutal match between Kara and Lee. Flashbacks from New Caprica reveal the origin and nature of their dispute.