Battlestar Galactica was not the only Battlestar to have survived the cylon attack, The Battlestar Pegasus also survived.

The Battlestars Galactica and Pegasus face a new Cylon target, a "Resurrection" ship, while a power struggle threatens to result in all-out war among the human fleet.

The struggle between Adama and Cain is temporarily put on hold while the two Battlestars combine forces for an assault on the Cylon Resurrection Ship. Apollo faces a momentous decision and Baltar takes an interest in Gina, the Cylon prisoner.

The untold story of Lee Adama's first mission as commander of the battlestar Pegasus begins as Lee asks Kendra Shaw to be his executive officer. Kendra—who's tough but troubled—was considered an exemplary officer by the Pegasus's original commander, the late Admiral Helena Cain.

Admiral William Adama assigns the Pegasus to find a Raptor that vanished during a scientific-research mission. At the Raptor's last known location, an armada of antiquated Cylon Raiders piloted by Centurions attacks the Pegasus. The captive Sharon identifies the old-fashioned machines as "guardians," a particular group of Cylons who experimented on humans during the first Cylon War.