When Adama orders all Colonial ships fitted with Cylon FTL technology, the rebel Cylons demand legal citizenship under Colonial law in return and the Quorum led by an adamant Tom Zarek fiercely oppose the deal. Meanwhile, Laura’s continued reclusion causes tension within the government, Tyrol learns a disturbing secret about Nicky, Tigh and Caprica-Six get a first look at their child, and Gaeta’s outspokenness over the alliance rouses murmurs of mutiny aboard Galactica.
Dualla's life has abruptly ended; yet the Cylon race is on the brink of a new start, pending the birth of Caprica Six and Saul Tigh's baby. And while they are optimistic over their new arrival, Gaeta's hatred towards the Cylons continues to rise. Then, a fluke illness leads the Chief to discover that not he – but Hot Dog – is Nicki's biological father.
Certain that the Cylons are the bane of human existence, Gaeta continually questions Kara Thrace's loyalty to the fleet and her intentions for humanity. Petulant and desperate for vengeance he decides to work against the Adama and Roslin administration, by any means necessary, in order to cease Cylon existence. He affirms that "one day soon, there's going to be a reckoning… and once again people are going to have to answer for what they've done."
Meanwhile Laura Roslin, still evading her Presidential responsibilities, leaves Zarek in charge and the Adamas at odds. When the Admiral, proposes the use of Cylon technology to complete a necessary FTL upgrade on all the fleet's ships, he is met with fierce opposition from Zarek, who rallies the Quorum of Twelve to vote with him against a human-Cylon alliance.
Leading his own coalition of rebels, Gaius Baltar, still heralded as sacred prophet, pits his followers against God – whom he totes as the reason for their suffering and pain. With impressionable minds, lacks of consciences and proper guidance from their government, the fleet's member's venture down dangerous courses.
And ironically, just as Roslin and Adama throw caution to the wind and decide to indulge in their love, Gaeta and Tom Zarek also form their own union. At odds with the state of mankind, the two team up for the start of a revolution they deem necessary, regardless of the countless lives that may be at stake.