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While Commander Adama deals with a newly assertive Council of Twelve's modification of his command, Baltar plots his escape.

The mysterious Ship of Lights reappears, hijacks Apollo and his viper in space and sends him on a quest to save the planet Terra during peace negotiations with the Eastern Alliance. One of the beings of light takes human form to guide Apollo, and makes him take on the appearance of a missing Terran named Charlie.

The crew of the Galactica struggle to fight massive fires on board caused by Cylon suicide incendiary attacks.

Apollo and Starbuck come across a vessel they think may have come from Earth and take it aboard the Galactica. On board are two adults and four children in a state of suspended animation. Adama disagrees with the Council of Twelve about opening the sleeping chambers, for that may mean endangering the humans within. When the adult male, Michael, wakes up, he finds it difficult to breath the air on board the Galactica. Apollo, Starbuck and Cassiopea decide to escort the Lunar Shuttle Avion to its destination, hoping to find out if the travelers home, Terra, may be related to the planet Earth.

Military engagements with the Cylons push the Colonial Fleet toward an ice planet, where a vanguard discovers a Cylon weapon capable of singlehandedly destroying the Galactica.

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.

When a large number of Colonial Warriors come down with a serious infection, Apollo and Starbuck must train a number of female shuttle pilots to fly Vipers for combat duty.

After traversing a large void in space, the Galactica and the refugee fleet discover the home planet of their species, Kobol.

Starbuck is framed for murder of a sports rival. Apollo suspects Baltar but Adama agrees to charge Starbuck and try him for murder until Apollo can come up with some proof that he didn't do it.

After the Twelve Colonies of Mankind were destroyed in a sneak attack by the Cylon tyranny, the last Battlestar Galactica leads a makeshift fugitive fleet on a desperate search for the legendary planet Earth.

During a celebration honoring Commander Kronus, Starbuck recognizes an old flame of his, Aurora and breaks off a date with Cassiopeia to follow his lost love to the Celestra. On their arrival, Starbuck and Apollo find themselves in the midst of a mutiny.

When the Galactica crew detects that a Cylon Basestar has swung around to attempt to intercept the refugee fleet, Commander Adama decides to attack.

While suffering from a fuel shortage, The Galactica finds the supposedly lost Battlestar Pegasus, led by the legendary Commander Cain.

After Baltar's attack is repulsed, the crews of the Galactica and Pegasus carry out an attack on the planet Gamoray to acquire fuel supplies.

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 indicating 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 enthralled by the new viper, but less enthusiastic about CORA, who bears a personality that grates on Starbucks nerves. Starbuck picks up two star-craft from hundreds of years vintage and in the process he is double-crossed and knocked unconscious by a smuggler of liquor. Starbuck later finds himself incarcerated on Proteus, a prison planetoid that is a surviving body from hundreds of such penal facilities scattered through the stars by the Colonies during the Cylon War, facilities that made munitions and liquor for the war effort. Proteus is now manned by the distant antecedents of its original guards and prisoners and continues to make ambrosia for Colonial warriors, even though hundreds of years worth of ambrosia have never left the planet - and the planet may not even survive, as a Cylon patrol that has detected Starbuck's now-stolen viper has spotted the planetoid while the stolen viper is being pursued by Apollo and Boomer.

Apollo crashes on the Wild West like planet Equellus after being pursued by four Cylon fighters. Taken in by a widow named Vella and her son Puppis, Apollo takes on crime boss La Certa and Red-Eye, a Cylon centurion turned formidable gunfighter who killed Vella's husband Martin.

After the Cylons 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.

When an old con meets Starbuck and suggests he is the warrior's father, there proves to be more following the elder than family ties.

Silver Spar Squadron is overtaken by a Ship of Lights and subsequently disappears. Investigating a red planet, Apollo, Starbuck and Sheba find a crashed starship and a lone survivor, the mysterious Count Iblis. After Sheba takes him on a tour of the Galactica and other ships in the fleet, the charismatic Count offers to perform three miracles of the Colonial's choosing if they will surrender leadership of the fleet to him.

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.

Count Iblis has delivered the Colonials' enemy, Baltar before the Council of Twelve. As the Colonials celebrate, Adama and Apollo come to the conclusion that the secret to Iblis' identity can only be found within the wreckage of the ship where he was first encountered.