The Galactica's scout ships find a Cylon baseship in the Lion's Head nebula, adrift and helpless. Apollo and Sharon (now flying under her new callsign, "Athena") lead a team onto the ship to explore. Among a multitude of dead Cylons, they find only five who are still, but only barely, alive.
Apollo and Athena hurry back to the Galactica with these prize prisoners. Doc Cottle quarantines them all for study and identifies the virus that has infected the Cylon ship. Humans are immune to this particular pathogen-- and so is Athena, as the mother of a half-human child. All other Cylons, however, aren't so lucky. While Cottle can design a vaccine that will halt the virus's effects, special antibodies in the Cylons' blood will soon destroy the vaccine. In other words, if the prisoners don't receive frequent new injections, they'll die.
Tempted by hope of receiving this dubious cure, the Cylon prisoner Simon tells the humans everything he knows. He explains that the virus can be transmitted through the Cylon resurrection process, then mentions that Dr. Baltar is alive and assisting the Cylons in their quest to find Earth. Adama and Roslin are stunned by this revelation.
In fact, deep in the heart of the Cylon fleet, D'Anna and Caprica Six have turned against Baltar. They believe that he knew about the virus all along and led them to the nebula in order to kill them. To make him confess, they torture him. Wracked with pain, Baltar flees to the comfort of the Six in his mind, who might offer his only hope for salvation.
Back on the Galactica, Lee Adama has a chilling brainstorm: if they maneuver the Galactica within close range of a Cylon resurrection ship and kill their Cylon prisoners, the infected prisoners will then download to new bodies, spreading the virus to the Cylon fleet in the process. The disease will then rage freely throughout Cylon civilization, eventually wiping out the entire race.
Shocked, Helo argues that the act is morally wrong. Admiral Adama shares his doubts. Athena grieves at the thought of her people's demise but tells Helo that she must remain loyal to her human comrades. Roslin, her duty to safeguard the survival of humanity foremost in her mind, believes that the genocidal attack might be justified. But as she prepares to make her decision, it is humanity's collective soul rather than its survival that is at stake ... .
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