Great Cylon Turkey Shoot
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Several weeks after leaving Kobol, Galactica begins to suffer various system failures and ship-wide malfunctions. Lieutenant Gaeta and Dr. Baltar suspect that the Cylon virus which infected Galactica (Scattered), and downed ship functions for a time (Valley of Darkness), has returned. They hypothesize that the virus had a latent component that hid itself, slowly emerging throughout ship computers, then testing and probing for system vulnerabilities.
Lt. Karl Agathon shows a printout of the virus to the incarcerated Caprica copy of Sharon Valerii, who concludes that this logic bomb is a prelude to a Cylon attack. Gaeta determines that the virus can be removed by erasing all ship computer hard drives, then reloading the computers from backups made before the war. However, this will leave the ship completely vulnerable for several minutes, giving the Cylons a perfect opportunity to do away with Galactica. Yet if they do not proceed with this course of action, the logic bomb could "detonate", likely taking control of the battlestar and turning it against the Fleet.
Reluctantly, Commander Adama elects to have Sharon aid them in combating the enemy. She interfaces with the ship's mainframe and communication systems—using a fiber-optic link placed within her left forearm—and prepares an electronic attack to ward off the Cylons.
Just then, a Cylon fleet consisting of hundreds of Raiders, descends upon Galactica. As the battlestar deploys all combat-ready Vipers, and Gaeta erases the ship's hard drives, Sharon copies the logic bomb's code onto herself, alters it, and transmits the re-programmed virus to the enemy. In a poignant turn of events, the entire Cylon fleet is disabled by the virus - much like Colonial warships were during the Fall of the Twelve Colonies.
Though many Raiders are wrecked by crashing into one another, Colonel Tigh orders Galactica's Vipers to open fire on the crippled enemy. Apollo jubilantly relays the weapons free order to his fighter group, and the Vipers proceed to tear through the jumbled Cylon formations, destroying the disproportionately larger Cylon force in its entirety (Flight of the Phoenix).
The presence of numerous Heavy Raiders within the attacking Cylon fleet, suggests that the Cylons intended to board Galactica—and possibly other Colonial ships—after the virus had rendered the battlestar helpless.