Command Navigation Program

The Command Navigation Program (CNP) was a software upgrade for all Colonial Fleet systems.  It was proclaimed as a massive step forward for the military, increasing combat effectiveness up to three-fold (some boasted that a nugget flying with the CNP would be the equal of an ace without it).  The CNP was created by Dr. Gaius Baltar and released in the months leading up to the Fall.

CNP Backdoors and "Virus"

The CNP is often mislabeled as a "virus".  The Cylons were known to use viruses to infiltrate and neutralize enemy systems, but that is not what occurred with the CNP.  The Cylons managed to alter the CNP's code and have it distributed with a hidden backdoor written into it.  This allowed the Cylons to send out a simple signal which would activate that backdoor and completely lock any CNP installed system.  This caused weapons not to respond, communications not to transmit, engines to stall, and in some cases even caused ship-wide power failure.  With the Colonial Fleet unable to fight back and often unable to even retreat, the Cylon forces made short work of the defenseless Colonials and thus accomplished in a few hours what they had failed to accomplish in the twelve years of the First Cylon War.

Surviving the CNP

Nearly the entire Colonial Fleet was destroyed thanks to the Cylon exploitation of the CNP's backdoors.  Those few that survived managed to do so because:

The CNP was never installed

Some ships merely survived because there was no backdoor to use.  Examples of this include aging Galactica and Augustus which were scheduled for decommission.  They had the CNP available to them but simply never installed it.

The CNP was offline

Other ships did have the CNP but at the time of the attack the CNP was not online or it was unable to completely lock them out because the systems were not completely networked with the CNP.  Examples of this include Battlestar Pegasus.  These ships were either at shipyards or on the ground at the time of the attack and not completely online.