The survivor count shown in the title sequence for Part 1 is 39,516. The survivor count shown in the title sequence for Part 2 is 39,406. At the end of Part 2, Admiral Adama announces the survivor population at approximately 38,000
The episodes portray the Galactica launching a rescue mission to retrieve Hera Agathon from the "colony", a heavily armed and defended Cylon base located near a black hole. They manage to rescue Hera, and in the end, the fleet finds a new planet to settle on, which they come to call Earth (revealed to be our Earth). The final episodes gave Battlestar Galactica the strongest ratings since its second season, though they received mixed reviews
The Galactica crew members and civilians divide themselves between those joining the rescue attempt, and those staying behind with the fleet.
The flashback sequences during the course of the first part take place a few years before the Cylon attack on Caprica. William Adama (Edward James Olmos) is reluctant to undergo a lie detector test in preparation for a civilian desk job. Elsewhere, Gaius Baltar (James Callis) is getting tired of his father, Julian, who is abusive to his nurse. However, Caprica Six (Tricia Helfer) soon informs Baltar that she took his father into a care home, where he will be happier. Laura Roslin (Mary McDonnell) is living happily with her two sisters, one of whom is pregnant. But later, Roslin receives distressing news that both her sisters and father were killed in a car accident. Three months after, she is set up for a blind date and is encouraged to join Mayor Adar's presidential campaign. Lee Adama (Jamie Bamber) meets Kara Thrace (Katee Sackhoff) for the first time while she is seeing his brother, Zak (Tobias Mehler). When Lee arrives home drunk, he notices a pigeon in his house, and he chases it away. Lastly, the flashbacks focus on Anders (Michael Trucco), who is interviewed during his sporting career, where he admits to playing for the joy of the pursuit of perfection rather than the winning.
Back in the present, Galactica is being stripped for parts to be used on other ships, while the military will be transferred to control the Rebel Basestar. The pictures of the fallen in the memorial hallway are also taken down. Baltar wants his people to have a seat on the quorum, but Lee refuses. Admiral Adama later decides to give amnesty to those who took part in the attempted coup d'état, as well as to Tyrol (Aaron Douglas), who is in the brig for helping Boomer (Grace Park) escape. This allows Tyrol to take part in the mission to retrieve Hera (Iliana Gomez-Martinez), who is being studied by the Cylons to determine how Cylons can reproduce. However, Adama doesn't allow Cottle (Donnelly Rhodes) to join in, as he says that the fleet cannot afford to lose a doctor. Several others join in the operation, including the original Cylon models, and a weakened Roslin. A Raptor is dispatched to the possible location of the "Colony", only to find it located very close to a black hole, but despite the circumstance, Adama orders an attack to begin.