The Galactica discovers the abandoned Cylon Basestar and learns that the Cylons have been infected by a virus they acquired from a beacon floating in space. The team returns to Galactica with some of the surviving but very ill Cylons. Dr. Cottle determines that humans are immune to the virus but Athena has to stay in quarantine. Cottle also determines that the virus is a fairly simple form of encephalitis for which he can easily create a vaccine. Apollo argues in favor of using the virus to destroy the Cylon race once and for all while Helo argues that to do so is a crime against humanity. In questioning one of the Cylons, they also learn that Baltar is alive and has given the Cylons his navigation charts. Meanwhile, Gaius Baltar's deception is discovered and the Cylons are prepared to dispose of him, but not before they get as much information as possible from him about the virus.
—garykmcd