Developed by Dr. Gaius Baltar, the Command Navigation Program (CNP) was a program utilized by the Colonial military forces of the Twelve Colonies and apparently by many civilian ships. Presumably installed in the central computers of Vipers and Raptors and in the navigation computers of almost all battlestars, it was a contrivance that was more than two years in the making.
Unbeknownst to Baltar, one of his lovers and co-writers of the CNP turned out to be a version of the Humano-Cylon agent Number Six. She also programmed backdoors into the program so that the Cylon attack force could break through the Colonial firewalls. Ships with the CNP that received a command from attacking Cylon ships would, in the case of the Vipers and presumably the Raptors, be shut down completely, "as if a switch were flipped," while battlestars suffered "mechanical failures" of various kinds, up to and including full shutdown.
The CNP was distributed as with all Colonial software updates via the Colonial Defense Mainframe, where Six had unrestricted access on Baltar's authorization.
The CNP was received by battlestar Galactica, but the program was never loaded into primary memory of the ship, although her last squadron of Viper Mark VIIs (led by CAG Jackson Spencer) did receive the upgrade. As a result, the squadron was massacred by two Cylon Raiders on their way back to Caprica (Mini-Series).
Lieutenant Felix Gaeta has the program code purged from the mainframe on Baltar's suggestion, and the program was also deleted from the flight systems of any of Galactica's surviving Mark VII Vipers and Raptors that had previously received the upgrade, as well as (one assumes) the systems of surviving ships (mostly Vipers and Raptors) that made their way to Ragnar Anchorage after William Adama took command of the Fleet.