The episode begins just after the final events of "Crossroads, Part 2." After encountering Starbuck in the Ionian Nebula, Apollo returns to the defense of the fleet against the rapidly closing Cylon forces.
On Galactica, only minutes after discovering their true identities, the four "Final Five" Cylons (Col. Tigh, Tory Foster, Samuel Anders and Galen Tyrol) suffer anxiety over what they might do. In the CIC, Tigh imagines shooting Admiral Adama, much as Boomer had done two years earlier.
On the flight deck, new Viper pilot Samuel Anders worries about turning against the other Colonial pilots when he and the other reserves are scrambled, but Chief Tyrol urges him to stay focused and launch.
The Colonial fleet begins taking heavy losses as Cylon Raiders and missile volleys begin to pierce Galactica's defensive perimeter. The civilian ship Pyxis is destroyed with 600 aboard and other ships are badly damaged. Anders finds his guns unresponsive when he tries to fire on a Cylon Raider. Anders appears momentarily paralyzed as the Raider swings around to face him, making direct eye contact. Anders' eye momentarily flashes with a red glow, like that of a Raider or Centurion. Suddenly, the Raider disengages, followed in turn by the rest of the Cylon fleet.
After Starbuck lands on the Galactica, she is bewildered when everyone looks suspiciously at her. She claims to have been gone for only six hours, but the crew believes her to have been dead for two months. Her Viper's tail number matches the one she was flying when Apollo saw her explode, but the craft itself appears to be brand new. While her gun camera has recorded images that appear to match the descriptions of Earth given in the Scroll of Pythia, the craft's navigational computer is blank with no records of her route back to the fleet.
Starbuck describes having a feeling of how to get to Earth, but that feeling begins to fade as the fleet makes faster-than-light jumps away from the Ionian Nebula. Starbuck appears to experience headaches when the fleet jumps, and she urges Admiral Adama to change course. He refuses, stating that he will continue on the path stipulated by President Roslin, the direction pointed to by the Eye of Jupiter.
Meanwhile, Gaius Baltar is received warmly by a cult that has erected a shrine to him in an unused compartment of Galactica. As the others leave, one of the young women stays behind with Baltar. She is fascinated by the way he appears to be praying with his hands clasped, although Baltar is really responding to Head Six. At the suggestion of Six, Baltar affirms for the young woman that there is only one God. She is overjoyed to have her beliefs confirmed and the two make love.
Shortly afterwards, Jeanne returns from the infirmary with her son who is very sick and near death. Once the group members have gone to sleep, Baltar prays softly to the one God to spare the child's life and take his instead. Jeanne wakens and listens to Baltar's plea silently, while crying.
Later on, Baltar and Paulla, one of the group members, are ambushed by two men including Charlie Connor. Connor blames Baltar for his son's death on New Caprica. As Connor holds a razor to Baltar's throat, Baltar speaks aloud to God, reiterating his desire to die in the sick child's place. Head Six appears and asks if Baltar really means it. Baltar says he does. Connor is surprised by Baltar's actions. Paulla escapes from Shaunt, the other attacker. She grabs a metal rod and incapacitates Shaunt. Then she attacks Connor and saves Baltar. Upon returning to the group's gathering place, Baltar finds the sick child has been miraculously cured.
Adama, Apollo, Roslin and Tigh discuss Starbuck's return from the dead. Apollo suggests that Starbuck's reappearance could in fact be their next clue to finding Earth, but Roslin believes it is another Cylon trick. On the CIC, Gaeta and Helo try to narrow down the location of Earth from clues in Starbuck's gun camera. Starbuck grows increasingly desperate as the fleet jumps further away from the Ionian Nebula, fearing she will lose her perception of Earth completely.
Starbuck and Anders share a moment in front of her picture on "Memorial Highway," which is still hanging among the dead and missing. Starbuck wonders if Roslin's suspicions are right and that she could in fact be a Cylon, or a clone – bringing up her mysterious surgery back on Cylon-occupied Caprica. Anders says that if she is a Cylon, then she has always been one. He tells her that if she were, he would still love her anyway. Starbuck lauds his devotion, but says that if Anders were a Cylon she would kill him without hesitation.
After another jump, Starbuck experiences more pain, and decides that the only way to turn the fleet around is to confront President Roslin. She overcomes two guards assigned to follow her and subdues a marine outside Admiral Adama's quarters where Roslin is staying. Roslin awakens to find Starbuck pointing a gun at her face.