Virus
A virus is a non-living pathogen with biological processes that can interrupt cellular activity. In computer terms, a virus can also be a set of programming instructions, surreptitiously inserted into another computer or network, that can interrupt or stop the functionality of other computer programs.
Re-imagined Series Usage
In the Re-imagined Series, the concept of the virus was generally left to the use of computer viruses by the Cylons to infect Colonial computers to force malfunctions that would render a ship vulnerable to attack.
The virus infiltration tactic was used greatly in the first Cylon War. In response, the Colonials began using simpler technologies that were impossible to reprogram or shut down. The first battlestars, of which Galactica is a member, used computers but didn't network them or tie them to external sensors or communications, preventing a virus from entering ship's systems and minimizing damage to other systems in the event of an infection. Comparatively primitive communications gear and other hardware throughout the ships also reduced or eliminated the ability of the Cylons to hack into or shut down a shipboard function.
In the Second Cylon War, the Cylons returned to their tactic of infiltration after their espionage determined that Colonial use of computer technology had become widespread once again, 40 years after the first war.
While the Colonial computers were likely resistant to viral infection because they could not be cracked from the outside, after Cylon agents created backdoors in the Command Navigation Program used by almost all Colonial military ships, the attacking Cylon fleet could transmit a signal through the backdoors programmed in the CNP, commanding the CNP to shut down or disable key elements of itself or ship systems. In a sense, instead of trying to break down the Colonial's "door" with a thug (a virus), the Cylons simply changed the door's locks so they could enter by an easier path.
The compromised CNP permits the easy destruction of Colonial defenses and slaughter of countless billions of Colonial citizens living on the Twelve Colonies.
Despite the efforts of decommissioning Galactica and converting it into a museum, the battlestar was still designed to withstand this tactic as this new Cylon war began. While her last squadron of Viper Mark VII's were infected and destroyed early in the initial attack (Miniseries), a squadron of Mark IIs onboard are redeployed. Like their carrier ship, these Vipers are also designed to ward off a Cylon infection or backdoor exploit, and hold their own against future Cylon attacks.
Galactica suffers an Cylon virus infection near the legendary planet of Kobol after doing what Commander William Adama (at the time, seriously wounded in an assassination attempt) would never allow: The temporary networking of several of the battlestar's computers to greatly reduce the computation time needed to find the proper coordinates of the missing civilian Fleet, which Jumped to a different set of coordinates (Scattered). Firewalls (software barriers that deny unauthorized intrusion) are put in place to slow down a Cylon hacking attack, but the protection loses its integrity at the very last moment. After the virus initially shuts down several systems (while, coincidentally, a squad of heavily-armored Cylon Centurions board Galactica), the battlestar uses software or other means to purge the virus (Valley of Darkness).
All appeared successful with the purge until weeks later when the virus returns, this time as a heuristic infection that formed itself as a "Logic bomb", threatening to deny control of the battlestar to its human crew and likely forcing the battlestar's guns on the civilian Fleet and activating the damage control systems to open vents to asphyxiate the crew. The virus is finally removed for good by wiping the hard drives of all computers and restoring them from backups made prior to the Cylon attack (Flight of the Phoenix).
The tables are turned against the Cylons once more in a strange juxtaposition of the concepts of the biological and cybernetic definitions of viral infection. The Cylons, many of which heavily integrate biological elements with their cybernetics, are infected with an ancient human pathogen, lymphocytic encephalitis, after a scouting basestar recovers a beacon left by the Thirteenth Tribe thousands of years before. The Cylon majority who receive reports of this infection immediately cut off communication with the infected basestar and take measures to ensure that the dying Cylon agents will not resurrect by moving their Resurrection Ship out of range. The virus is rampant; it directly infects the Cylon agents on the basestar, and by logical extension, the Hybrid. As the Hybrid controls or is in communication with the Raiders and Cylon Centurions, these units, too, receive the infection and are disabled.
The Cylons believe that there was a bioelectric component to the virus that also infected the consciousnesses of these dying agents; a downloaded agent's consciousness could have the virus (now incorporated as a computer virus within the agent's downloaded consciousness) that could spread to all Cylons. The results would have been catastrophic; with no cure or immunity to the virus (as humans have developed over the millenniums), the Cylon race would be wiped out. The Colonials realize this point after exploring the infected basestar and learning of the infection through a handful of sickened Cylon survivors. President Laura Roslin authorizes the use of the captured dying agents as a form of biological weapon. Once Galactica found the larger Cylon fleet (guarding their Resurrection Ship nearby), the Colonials planned to kill the dying agents, forcing their consciousnesses to download back to the Cylons, which would infect and eventually kill the entire Cylon populace. The plan is aborted after sabotage kills the agents before Galactica was close enough to the Cylon fleet (A Measure of Salvation).
Original Series
In the episode, "Lost Planet of the Gods, Part I", the dominantly-male contingent of Colonial Warriors are downed by an infection that enters the group after Boomer skips the required decontamination procedures. The situation becomes so bad in terms of the Fleet's defense that female shuttle pilots are pressed into service as Viper pilots. Dr. Salik finds a cure while the new recruits stave off a serious Cylon advance.