The Twelve Colonies of Man are annihilated by the Cylons. Adama, commanding the last surviving Battlestar, takes it upon himself to lead all remaining survivors aboard 220 ships to find a new home. After the Galactica's fighter pilots successfully navigate a path through the Nova of Madagon minefield, the spoiled Sire Uri proposes to settle down on Carillon, where food and entertainment are provided by the natives. However, Adama suspects a Cylon trap.
Out on patrol, Apollo and Starbuck come across a great void, while Boomer and Jolly are infected with a plague that soon infects the remaining Viper pilots. Soon, Apollo and Starbuck find themselves having to train a group of female cadets, including Apollo's fiancée, Serina.
Adama orders the fleet to set a course into the seemingly endless void, where he expects to find the lost planet of Kobol, mother-world of the twelve tribes of man. Apollo and Serina are 'sealed' in marriage while Starbuck is being held captive on Baltar's Basestar. When Baltar learns of the search for Kobol, he follows the Colonial fleet for a face to face confrontation with Adama.
Apollo crashes on the Wild West like planet Equellus after being pursued by four Cylon fighters. Taken in by a widow named Bella and her son Puppis, Apollo takes on crime boss La Certa and Red-Eye, a Cylon centurion turned formidable gunfighter who killed Bella's husband Martin.
Starbuck's unplanned double-date with Cassiopeia and Athena on the recently-reopened luxury liner Rising Star is interrupted when the Galactica picks up long-range transmission traffic indicting human life in a distant solar system on the other side of a vast asteroid dust field. Starbuck is recalled to duty to pilot the Starchaser, an up-powered reconnaissance viper denuded of weaponry and bearing a voice-activated computer - Computer, Oral Response Activated, known simply as CORA - that can handle the vast increase in performance in the new viper. Starbuck is ...
A special task force, mostly made up out of convicts, is dispatched to destroy a giant Cylon operated pulsar cannon on the planet Aracta directly in the Colonial Fleet's path. Having lost a cadet on the planet earlier, Starbuck is eager to join the expedition for once. Boxey and Muffit also join the group as stowaways.
As Apollo and the team of convicted specialists brave the snowy mountain to blow up the Ravashol Pulsar, the criminals plan their escape. Starbuck is still determined to make a detour and rescue cadet Cree, but the Theta clones object to the destruction of their creator's weapon.
After the Cylon's destroy two of the fleet's Agro ships and cripple the last remaining one, Adama hopes to swap an old energizer for seed on the the planet Sectar in Quadrant Zeta. Unfortunately Siress Belloby won't give up the energizer unless the commander courts her. Down on the planet, the inhabitants of the small Agro community of Serenity are looking for a new dispensable constable to hold off the Borays who raid the town each high moon.
Shot down by Cylons, Starbuck crash lands on Attila, a planet on the far edge of Omega Sector and finds himself rescued from a phalanx of Cylons by a family of children. Kyle, the young leader of these self proclaimed warriors, soon hatches a plan to trade Starbuck to Outpost commander Spectre for his captured father.