In the episode, President Laura Roslin orders Sharon's pregnancy terminated. The order is suspended after Gaius Baltar discovers that the fetus's blood can cure Roslin's cancer, which it does. Baltar aligns himself with an underground group of Cylon sympathizers whose ranks include the troubled Number Six copy Gina.
Roslin lies near death in Galactica's sickbay. Doctor Cottle reports abnormalities in Sharon's unborn child's blood. Believing the child a threat to the fleet, Roslin orders her pregnancy terminated over Baltar's objections. Head Six, who regards Sharon's child as hers with Baltar, appears to Baltar and insists he intervene. Roslin's decision outrages Sharon and Helo, the child's father, who obstructs the entrance to sickbay. Baltar defuses the standoff by announcing that a transfusion of the fetus's abnormal blood may save Roslin's life. The procedure cures Roslin's cancer within days.
In a sequence of delirious flashbacks, Roslin recalls negotiating an end to a teachers' strike on Caprica as Secretary of Education. Her conciliatory approach angered then-President Richard Adar, with whom she was having an affair, but she refused to back down. She also recalls seeing Baltar with a Number Six shortly before the Cylon attack on the Twelve Colonies.
A civilian crew member sabotages some ammunition. An investigation reveals she is a member of Demand Peace, an underground group of Cylon sympathizers. Admiral William Adama feigns negotiation with Demand Peace only to arrest its representative, Royan Jahee, when he arrives on Galactica. Demand Peace bombs a fuel refinery ship. Roslin meets with Jahee, agrees to hear his group's case, and warns that further violence will lead to harsh measures.
Baltar meets secretly with Gina on Cloud Nine. Gina rejects his sexual advances but invites him to join Demand Peace; Baltar refuses. Head Six laments that saving Roslin's life prevented Baltar, who is Vice President, from becoming President. Baltar concludes from a letter Roslin wrote to him in the event of her death that she will never trust him. Jahee returns to Cloud Nine and presents Gina with a gift from Baltar: a nuclear warhead Adama provided Baltar for research purposes in an earlier episode.