Survivor Count: 41,420.
The fleet has found a Cylon Basestar adrift in space and the Galactica sends a wing of Raptors and Vipers to investigate. Major Apollo leads a boarding team inside the ship. They discover most of the Cylons are dead, however a small group is found barely alive on the bridge. The landing team also finds the mysterious cylinder device. Sharon "Athena" Agathon tries to access the Basestar's computer system to no avail. She then speaks with a Cylon copy of herself who calls her a traitor. Apollo requests permission to finish off the Cylons. However, at Captain Helo's suggestion, Admiral Adama orders the prisoners to be brought back to Galactica for interrogation. As the boarding party leaves the Basestar, it explodes, presumably by means of an auto-destruct mechanism. The strange device is destroyed with it.
Back at the Cylon fleet, Gaius Baltar is confronted by Number Three and Number Six, who ask why he didn't reveal the existence of the device he found on the Basestar. Baltar feigns ignorance at first, but then confesses that he did know about the device, and apologizes for not mentioning it sooner. Three and Six believe that he knows more about the device than he's letting on. They have two Centurions take him away for interrogation.
On Galactica, the Cylon prisoners, as well as Apollo's boarding party are placed under quarantine by Doctor Cottle. Later, he determines the virus to be a strain of Lymphocytic Encephalitis, one that has caused the Cylon's brains to swell and other symptoms like high fever, stupor and disorientation. Humans, however, are immune to it, so Cottle releases the pilots from quarantine but tells Athena to remain.
Cottle reports to Adama and President Roslin that he can create a serum that will suppress the virus and keep the Cylons alive, without ever curing them; the Cylons will have to be given periodic injections to keep them alive. A Cylon copy of Simon is brought before Adama and Roslin. In exchange for the serum, Simon explains the Cylons' plans to find Earth. He reveals that Baltar is with the Cylon fleet and is showing them the way to Earth. Simon further explains about the probe, and how the contaminated Basestar was abandoned by the rest of the Cylon fleet.
Apollo realizes that the human race now has a way to exterminate the Cylons once and for all. All they need do is execute their Cylon prisoners within range of a Cylon Resurrection Ship. The virus will download to that ship, and thereby spread to the rest of the Cylons race. Captain Helo objects to this plan, arguing that exterminating an entire race would be a "crime against humanity" and make the humans no better than the Cylons. Apollo argues that the Cylons are not human and they should be wiped out. Helo retorts saying that Sharon ("Athena"), his wife and a Galactica officer, has proved her loyalty, risking her neck time and again to help the human survivors and believes there may be more Cylons that think as she does.
Back at the Cylon fleet, Gaius is subjected to torture by Number Three. Baltar's mind wanders to a scene where he lies on a serene beach with Head Six. Fighting back waves of pain, Gaius tells Six that he knows nothing of the viral device's origin, but Six tells him to only think of her and to let his intelligence come up with the answers that Three wants to hear.
Elsewhere, Cottle releases Sharon from quarantine - her body contains cells from having carried a half-human baby (Hera), giving her immunity. Helo tells Athena of Apollo's plan to exterminate the Cylons with the virus and how it is eating away at his soul. Sharon asks if even a human would be able to keep her word (having been sworn in as a Galactica officer) when her entire race is about to be wiped out.
Adama meets with Roslin on Colonial One to discuss the proposal to wipe out the Cylons. Roslin is in favor of the plan, but Adama is uneasy, pointing out that he needs a Presidential Order to use biological weapons. Roslin sees through this as Adama's way of "passing the buck", a point that Adama readily concedes. Roslin takes the responsibility, and orders Adama to carry out the plan to destroy the Cylons with the virus.
Back on the Basestar, Baltar continues to be tortured by Number Three who demands he tell her what he knows. Gaius's mind however drifts in and out between the torture room and the beach with Six, who begins to make love to him. In between intense pain and erotic pleasure, Baltar talks of religion and faith, a monologue that makes little sense to Three because Gaius is actually talking to the Six in his head. He tells Six he loves her but Three doesn't realize who he is talking to, and she ends the torture with a look of pity on her face.
Galactica jumps away from the Colonial fleet and appears in a location within the Cylons' detection range. A Cylon fleet, complete with Resurrection Ship, duly appears. Adama orders Apollo to execute the Cylon prisoners, but when Apollo arrives at their cell, he discovers that the Cylons are already dead. Adama immediately recalls the Galactica's fighters and the Galactica jumps away.
The Cylons were in fact killed by Helo, who had secretly sabotaged the air handlers to remove the oxygen from their cell. Expecting to be arrested at any moment, Helo confesses his actions to Athena. He tells Athena that he believes he has made the right decision. However, the dreaded knock at the door of his quarters never comes.
Adama tells Roslin that the Cylons were killed before they had a chance to download to the Resurrection Ship, and that the plan to infect the Cylons with the virus has failed. Roslin believes there are only two possible suspects and asks what Adama is going to do about an investigation. Adama refuses to pursue the investigation any further, however, and tells her that he considers the matter closed. Their discussion switches to the mysterious probe. Adama says that Doctor Cottle believes that the contamination of the beacon was probably unintentional (in real life, LCM virus is fairly common), and that the virus from the beacon is a strain that existed 3000 years ago — around the same time that the Scriptures say the Thirteenth Colony left Kobol. Adama believes the device was a marker, and that they are definitely on the right track to finding Earth. Roslin agrees with this, but points out that if the humans are on the right track to Earth, then the Cylons must be too.