The episode primarily takes place on Cylon-occupied Caprica. After the Fall of the Twelve Colonies, the copy of Number Six (Tricia Helfer) that was responsible for disabling the Colonial defence system (affectionately known as "Caprica-Six") and Sharon "Boomer" Valerii (Grace Park) were both "downloaded": a standard Cylon practice of rebirth which takes place if a model is to perish, and have both been hailed as Cylon heroes due to their efforts in infiltrating human society.
Both are having difficulties in adjusting to life on Caprica. In particular, Caprica-Six is having visions of Gaius Baltar (James Callis) that only she can see, much like Baltar's visions of Caprica-Six, and Boomer is having problems accepting her Cylon nature to the point of the denial, even in danger of being "boxed", which means storing a Cylon's memories without consciousness out of its body. Number Three (Lucy Lawless) asks Caprica-Six to help Boomer in this regard. However, when Caprica-Six starts to associate more with Boomer, they both realize that the holocaust the Cylons effected was a sin.
Caprica-Six and Boomer are next shown conversing with Number Three. While the three move up a stairwell, explosives set by the resistance led by Samuel T. Anders (Michael Trucco) detonate, trapping Anders, Three, Boomer, and Caprica-Six in a parking garage. While Anders is originally shielded and hidden by the blast, Caprica-Six is injured, so much so that Number Three tries to euthanise her before finding Anders, whom she tries to kill instead. Number Three goads the other survivors so much that Caprica-Six kills her and forms a pact with Boomer to attempt to change Cylon opinion of humans.
The episode's secondary plot takes place on Galactica. The copy of Number Eight that defected from the Cylons gives birth by caesarian section to a baby whom she and Karl Agathon (Tahmoh Penikett) name "Hera". However, President Laura Roslin, and her secretary, Tory Foster, and Dr. Cottle conspire to fake Hera's death fearing what would happen if the Cylons knew the child lived. President Roslin also did not want Hera to be raised by her Cylon mother, Sharon, whom she still does not trust. At the end of the episode, the child is given to a woman who believes the child was born on Pegasus, while Helo and Chief Tyrol (Aaron Douglas) scatter the ashes they believe to be Hera's into space.