The episode guest starred actress Nana Visitor, best known for her role as Kira Nerys on Star Trek: Deep Space Nine. The survivor count shown in the title sequence is 39,675.
The episode begins aboard the Demetrius, as Helo refuses to obey Captain Starbuck's orders to rendezvous with Leoben's Basestar. Starbuck tries to initiate the FTL jump herself but is restrained by Athena. Helo tells Gaeta to initiate the jump to the fleet, but Anders prevents it by shooting Gaeta in the leg. Anders forcefully reminds Helo that Starbuck is still in command.
Horrified by the outcome of the situation, Starbuck finally agrees that taking the Demetrius is too risky and will instead take a Raptor. Anders volunteers to go with her, and Starbuck asks Athena to go as well, hoping she will alert them of any traps. Helo states the Raptor doesn't have enough fuel to return to the fleet, but Starbuck believes she can return with the Basestar. Helo gives her a 15 hour window before he returns to the fleet.
On Colonial One, President Roslin talks with her aide Tory Foster. She commends Tory, who has stepped up with more confidence in her duties and asks her to keep an eye on every issue. Because of her declining health, Roslin is unable to handle every detail herself.
Meanwhile, Starbuck's Raptor jumps to the middle of a Basestar graveyard. As she searches, Starbuck feels close to something and guides the Raptor to the sight of a ringed gas giant with three stars and a comet – the comet being, to Starbuck's astonishment, Leoben's Basestar as it trails vapor behind it. Suddenly, the Raptor is struck by debris and Starbuck is knocked unconscious.
Starbuck awakens, finding herself inside a Basestar hangar bay. While Athena inspects the Raptor, she is approached by several copies of the Number Eight model. One of them tells her that she was the first to realize their kind need not be a slave to their programming. They explain that in their attempt to revolt, the Sixes only led them to disaster and they ask Athena to help lead a mutiny against them. Athena refuses to get involved and admonishes the copies about picking a side and staying with it.
In Galactica's sickbay, Roslin overhears a terminal cancer patient, Emily Kowalski, complaining about her treatment. She finds her listening to Gaius Baltar over the radio, and suggests Emily's treatment would go better if she did not listen to him. Emily suddenly explodes in rage and tells Roslin to go away.
Back on the Basestar, Leoben argues with a Six (Natalie) over allowing Starbuck to see the Hybrid. Starbuck sees no choice in the matter as both sides need to help each other. Athena interfaces with the Cylon computer and informs that the Basestar's FTL is damaged. The system can piggyback off the Raptor's FTL to navigate a jump back to the Demetrius, but the Hybrid will have to be disconnected. After observing Athena's interface, Anders eyes another terminal. He inches his hand toward it covertly, but Starbuck calls his attention elsewhere.
As Anders' associate, Jean Barolay, preps the Raptor for the FTL link up, a copy of Six approaches and recognizes her as a resistance member back on New Caprica. The Six reminds Jean that she had murdered her, unprovoked, in cold blood. When Jean replies that she would be happy to do it again, the Six slams her head into the Raptor door frame. Jean stumbles and collapses, dead. Infuriated, Anders forces the Six to the deck and holds a gun to her head. Starbuck tries to talk Anders down from killing her. The Six known as Natalie asks her sister why she killed Barolay. The Six tells her of an incident on New Caprica when Barolay pushed her into a water treatment reservoir and did nothing but watch her drown, and that she could not get past it. Natalie reaches for the gun and while it is still in Anders' hands, she pulls the trigger herself. Natalie tells a stunned Anders that she gave him what he wanted – "blood for blood", and with no Resurrection Ship, she says the Six is as dead as his friend.
Back on Galactica, Roslin talks again with Emily who apologizes for her earlier outburst. She tells Roslin that she doesn't agree with Baltar's political stance, but agrees with his religious beliefs saying that she feels a single loving presence from God just as Baltar describes it. She says she had a dream of standing on a ferry boat, crossing the river that Baltar says separates their world from the afterlife. On the shore, she sees her family waiting for her.
On the Basestar, Starbuck sees the Hybrid and listens to her strange rant of technical information and nonsensical statements. Athena and a Number 8 arrive to disconnect the Hybrid; as the Number 8 proceeds to pull the connector, the Hybrid begins to howl. A Centurion guarding the room quickly reacts and shoots the Number 8 in the ensuing confusion. As Kara and Athena disable the Centurion with multiple gunshots, the Hybrid speaks to Starbuck: "The dying leader will know the truth of the opera house. The missing three will give you the five who have come from the home of the thirteenth. You are the harbinger of death, Kara Thrace. You will lead them all to their end. End of line." Starbuck stares into the face of the Hybrid, horrified by what she has been told.
On Galactica, Roslin sits with Emily. Roslin explains that Baltar is speaking only of the Cylon God, but Emily believes he is the god of all and argues that the metaphysical stories of the Lords of Kobol are inconceivable. Roslin agrees, stating the Lords are only metaphors. Roslin tearfully harkens back to when her mother was dying and how she believed Aphrodite would take her away, but in the end there was nothing but darkness. Emily says that Roslin was the one who saw only darkness and couldn't possibly know what her mother really experienced.
Back on the Basestar, Natalie tries to solve the Hybrid's riddle saying "the Three" is reference to D'anna and that she knows who the final five Cylons are. The five have come from the 13th tribe and they will know where Earth is. The next step is to unbox D'anna. Now knowing what to do, Starbuck's team and the Cylons prepare to rendezvous with the Demetrius.
On Galactica, Roslin has the dream that Emily described. Seeing herself on a boat with Emily and her loved ones waiting by the shore. Roslin sees her mother standing there for her, but responds that she is "not ready". She awakens to find that Emily has died.
On Demetrius, the clock has run out and Helo prepares to jump back to the fleet. Suddenly, the Basestar appears right on top of them. Athena calls Helo and tells him they have successfully secured the Basestar.
On Galactica, Roslin talks to Admiral Adama, discussing Emily's shared dream she had. Adama doesn't know what to make of it; his thoughts are set on Lee turning in his wings for a political career, and Starbuck's sudden reappearance from the dead. Knowing the Demetrius is overdue, Adama wonders if he will ever see Starbuck and her crew again. Roslin explains that she is with him now and that they will find Earth. Adama recollects when he only was using the myth of Earth as a carrot for the fleet. Roslin asks why he now believes in Earth, and he replies, smiling, she made him believe.