The survivor count shown in the title sequence is 39,556
Ellen Tigh and Boomer arrive at the fleet and Boomer is immediately taken to the brig. Ellen and Saul reunite and, after making love, go together to visit Sam Anders, who is still comatose. Tory Foster, Galen Tyrol, a Six and an Eight are also by Anders' bedside. The Cylons propose that since Ellen has returned, they should leave the human fleet, especially since Caprica Six is pregnant with Saul's fully Cylon child and they no longer need humans in order to reproduce. Ellen did not know about Caprica Six being pregnant, and is angry at Saul as she was never able to conceive children, and Caprica could only have become pregnant if he truly loved her. Furthermore, because the other Cylons are the Final Five's creations, she views Saul's relationship with Caprica in an incestuous light.
A vote is had by the Final Five on whether they should stay with the human fleet, and they promise to be bound by the results of that vote. Tory Foster and Galen Tyrol vote they go, Saul Tigh votes they stay and they assume from what Anders has said previously he would also vote to stay, which leaves Ellen with the deciding vote. She states that she needs more time, and goes to visit Caprica Six in her quarters. She "accidentally" tells Caprica Six that she and Saul had sex, before telling her she believed Saul loved Caprica more than he loved her. Ellen then calls another meeting, and says she has decided that the Cylon fleet should leave. Saul refuses to leave, and Ellen says this is because he loves the ship and William Adama more than herself or Caprica Six. Caprica becomes upset and starts to lose the baby. He and Ellen unite to try to tell Caprica that Saul does love her which Ellen believes will save the baby, but Caprica Six still suffers a miscarriage. Saul goes to Adama for support, revealing that the baby's name was "Liam", short for William. (Writer Jane Espenson confirmed that Saul wanted to name his child after his best friend.
Elsewhere, Tyrol and teams of Cylons attempt to fix the ship by using a Cylon polymer to grow into the cracks. Gaius Baltar rejoins his believers, who have taken up arms in order to get and keep supplies, but gives some away to starving people in "Dogsville" before the rest is stolen by the Sons of Ares. He appeals to Admiral Adama, who supplies him with weapons to prevent it happening in the future. Near the end of the episode, the monitor near Anders indicates that he has higher brain functions and his eyes flutter as in REM sleep. The episode ends with Roslin and Adama walking through the ship past a Six and an Eight working on the ship's hull and a group of mixed human and Cylon pilots. A Six has stopped in front of the Wall, staring at the photos, and Roslin realises that the Cylons have begun memorialising their dead there in the same way as the humans