- Midway through Season Two, the Galactica encountered another Battlestar that survived the Cylon attack: the Battlestar Pegasus. It's a much newer ship than the Galactica, is twice as big, has a ship-building facility onboard, and superior firepower.
- Pegasus is commanded by Admiral Helena Cain, an iron-fisted woman who defines the term "hardass." She's skeptical of everyone and everything, and doesn't tolerate anything less than perfection.
- Cain's Executive Officer is Colonel Fisk, who serves as the whip for Admiral Cain. He drunkenly tells the Galactica's Colonel Tigh that Cain killed her previous XO for not following orders. It's unclear if he's joking or telling the truth.
- The Pegasus has a Cylon Number Six model in captivity in their brig. This model is later freed by Baltar, and she executes Cain with a point-blank shot to the forehead.
- Colonel Fisk assumes control of the Pegasus after Cain's death, but is later killed by a man running a large black market in the Colonial fleet. After he dies, Chief Engineer Barry Garner assumes control, although he quickly proves that while he's a whiz at solving engineering problems, he's not much of a commander. He dies saving the ship, after which Admiral Adama promotes his son Lee to commander, and gives him the Pegasus as his first command.
- Commander Lee Adama sacrifices the Pegasus in order to save the Galactica and the Colonists fleeing from New Caprica. The ship is destroyed in a massive firefight, although the crew is able to abandon ship.
- Razor takes places between seasons Two and Three: Lee Adama is the commander of the ship, but through a series of flashbacks we're told how the Pegasus evaded destruction during the initial Cylon attack, and what happened to them up until their encounter with the Galactica.