In flashback sequences, William Adama and Saul Tigh (Michael Hogan) celebrate their upcoming retirement, where Tigh convinces Adama to take his new job. Later, as Adama is questioned in an interview, he complains that no job is worth questioning his loyalty and decides to rejoin the military. Lee has dinner with Zak and Starbuck again. When Zak passes out, drunk, the sexual tension between Kara and Lee nearly erupts before they are interrupted by a stirring Zak. Back home, Lee again encounters the pigeon, but this time he does not chase it. Roslin meets her blind date, who happens to be a former student of hers. After they go back to her apartment, she has second thoughts and ends the date; she then calls Adar's campaign, informing them of her intention to join it. Boomer meets Adama and Tigh for the first time, where she is warned that she is on the verge of ending her career due to her inability to land a Raptor. Given one last chance, Boomer gratefully tells the two that unlike other pilots, she will repay Adama one day. Meanwhile, Baltar, believing that Caprica Six is a corporate spy, allows her access to the military defense mainframe. He says that he is not doing this for her employers, but for her.
Back in the present of the series, Baltar decides to join the mission with Caprica Six at the last minute; she later admits to being proud of him for the first time. It is later revealed that Baltar's Inner Six, and Six's Inner Baltar are aware of each other, and the two real-life counterparts can see both of them. Romo Lampkin (Mark Sheppard) becomes the new president, and Hoshi (Brad Dryborough) is given command of the fleet while Adama and Galactica set off to rescue Hera. Galactica jumps right next to the colony, where they are immediately fired upon. Some of the Raptors, which are armed with nuclear weapons, make a short jump into the debris field and fly toward the back of the colony; in the process, Racetrack (Leah Cairns) and Skulls (Collin Lawrence) are killed by an asteroid. Anders has been installed into the CIC computers, and disables the Hybrids (Tiffany Lyndall-Knight). Galactica rams straight into the colony, where a strike team led by Starbuck searches for Hera. Hera is rescued by Boomer, who kills Simon (Rick Worthy) and finds Starbuck's team. Boomer hands Hera over to Athena (Grace Park) and tells her to, "tell the Admiral I owed him one." After her daughter is returned, Athena kills Boomer.
However, after Hera is returned, Galactica must also contend with numerous Cylon boarding parties. Hera is split off from her parents. She is spotted by Roslin, who takes a break from assisting with a triage, and is able to hide her from the Cylons, until she disappears again. While Roslin gives chase, Baltar and Caprica also spot Hera and give chase as well. The chase parallels the Opera House vision shared between Athena, Roslin and Caprica. The chase ends in the CIC, where Cavil (Dean Stockwell) holds her hostage. Inner Six and Inner Baltar again appear jointly to Baltar, inspiring him to make a speech saying, among other things, that he sees angels and convincing Cavil to end the war. The Cylon representatives agree that Cavil will give Hera back and let them leave if the Final Five give Cavil the technology for resurrection.
The Final Five begin the download of the technology for resurrection, with Saul and Ellen Tigh (Kate Vernon), Tory Foster (Rekha Sharma) and Galen Tyrol (Aaron Douglas) dipping their hands into Samuel Anders' (Michael Trucco) amniotic fluid to transfer the data to the Colony. But as they download the info, they can see each other's memories. Tyrol is made aware that Tory murdered his wife, Cally, and kills her in revenge before the downloading is complete. Feeling betrayed, the Cylons resume fighting; after the other Cylons in CIC are killed, Cavil commits suicide. In the debris field, a chance rock strike causes Racetrack's hand to fall on the launch button for her Raptor's nuclear weapons; the missiles strike directly into the colony, knocking it out of orbit. With Galactica being dragged toward the singularity along with the colony, Adama orders Starbuck to jump the ship away, anywhere. Starbuck finds herself entering coordinates into the computer as if she were playing a song, using the notes which Hera had written. Galactica jumps away and out of danger, leaving the colony to inevitably fall to its destruction within the black hole.
Galactica arrives at Kara's mysterious coordinates, its final destination as the damage caused in the battle has rendered the ship incapable of surviving any further jumps. Miraculously, the Galactica finds itself in orbit around a habitable world: our own Earth.
Hours later, the rest of the fleet has been summoned. Lee makes the unorthodox suggestion that they abandon their technology and start afresh, while Adama and others discover primitive humans already occupying the planet. Since finding Earth was always the goal of the Colonial Fleet, Adama suggests they call this planet Earth. The survivors - Galactica's crew, the remaining inhabitants of the fleet, and the Cylon Twos, Sixes and Eights - take basic supplies and spread out across the planet - not to colonize it but to blend in with primitive early humans, leaving Anders to fly the fleet into the Sun. The decision was made not to colonize this time, but to break the cycle. "All this has happened before..." but maybe it won't happen again. Leave it all behind and start over. "We can give them the best part of ourselves, but not the baggage". The Rebel Cylons decide that their Centurions have earned their freedom, and give them control of the Basestar, which jumps away to parts unknown. Starbuck, her destiny completed, literally vanishes without a trace after saying goodbye to Lee.
Baltar and Caprica Six are visited by their Inner messengers, who inform them that their destinies - to save Hera - have been fulfilled, and the two decide to live out the rest of their lives together. Lee expresses his desire to venture off and explore the planet. Tyrol decides to settle by himself on a remote northern island (implied to be the Scottish highlands). Helo (Tahmoh Penikett), Athena and Hera are reunited as a family. Tigh and Ellen stay with the rest of the survivors. Adama leaves with Roslin, but while admiring the wildlife and looking for a place to build a cabin for them, Roslin dies peacefully. Adama finds the place where he will build the cabin, and buries Laura on a nearby hillside.
New York City, 150,000 years later: humanity has reached the early 21st century, and the development of robotics and computerization continues unabated. Inner Baltar and Inner Six (no longer tied to the long-deceased Gaius Baltar and Caprica Six) comment on the recent discovery of what is believed to be "mitochondrial Eve" in Tanzania... the remains of Hera Agathon, progenitor of modern day humanity. Inner Six disagrees with her counterpart about humanity's next future: when a complex system repeats, something new is bound to happen, and this Earth - descendant of devastated planets Kobol, Caprica and the original Earth - may escape the vicious circle of technology, all part of God's plan. "You know it doesn't like that name," Inner Baltar replies, as the two stroll away