In the episode, Cylons capture Kara "Starbuck" Thrace and hold her in an abandoned hospital, where they are performing experiments with human reproduction. Starbuck escapes and leaves Caprica to return to the human fleet. Commander William Adama returns to command of the fleet, but President Laura Roslin persuades almost a third of the fleet to follow her back to Kobol.
Starbuck wakes up with Sam Anders. He tries to persuade her to stay on Caprica, but she insists on returning to Galactica. She recommends the resistance give up fighting, move to higher ground, and wait for her to return with a rescue party.
Cylons ambush the resistance as they make plans to capture a Cylon Heavy Raider. Starbuck is shot and loses consciousness. She wakes in a hospital, where a doctor named Simon tends her. Simon explains that Anders brought her to the hospital but later died from a shrapnel wound. Simon laughingly dismisses Starbuck's suspicion that he is a Cylon and explains away her other concerns. He presses the idea that Starbuck have a baby, calling child-bearing women "a very precious commodity to us." Starbuck demurs.
Meanwhile, Anders, very much alive, leads a search party. Caprica-Boomer appears and promises to take them to Starbuck.
Starbuck is kept heavily sedated. She is suspicious after an unplanned emergency surgery following a pelvic examination, and her suspicions are confirmed when Simon calls her "Starbuck", a name she never revealed to him. Starbuck fakes sedation and sneaks out of her room, where she sees Simon talking to a Number Six copy. When Simon returns, Starbuck kills him by stabbing him with a fragment from a broken mirror. Searching for a way out, she discovers other captured human women, attached to machines. One woman, a member of the resistance, says they have become "baby machines" and "can't live like this." Starbuck breaks the Cylon equipment, killing the women. Fleeing, she encounters another copy of Simon, confirming that he is a Cylon. The resistance rescues Starbuck with the aid of Boomer, who provides close air support from a Heavy Raider.
Boomer explains that the Cylons have had no success reproducing on their own and are trying to reproduce with humans. Appalled, Starbuck volunteers to stay and help liberate these so-called "Farms". Anders reminds her of her mission, and she reiterates her promise to return with rescue. She departs in the stolen Heavy Raider to return to the human fleet.
The human fleet
Commander Adama returns to command and orders a ship-by-ship search for Roslin and Lee "Apollo" Adama, who are still on the run. After Apollo finds himself unable to go through with Tom Zarek's suggestion that he denounce his father publicly, Roslin sends a message to the fleet asking anyone who believes in the prophecies to follow her to Kobol. Commander Adama dismisses the message as "religious crap" and is astonished when almost a third of the fleet follows her.
Chief Galen Tyrol says Galactica-Boomer was just a machine, but Commander Adama insists she was more than that. Adama reminds Tyrol that the Cylons will resurrect Boomer and tells him Specialist Cally will spend 30 days in the brig for shooting her. Adama views Boomer's corpse in the morgue and weeps over her.