Unbeknownst to Dr. Baltar, his lover and co-writer of the CNP turns out to be a version of the humanoid Cylon known as Number Six.
Installed in the central computers of Vipers and Raptors and in the navigation computers of almost all battlestars, the CNP was more than two years in the making
The Cylon infiltrator programmed backdoors into the CNP so that the Cylon attack forces could render any ships that use the operating system to shut itself down by a remote command.
Battlestars and fighters begin to shut down during the Colonial defensive "as if a switch were flipped." Communications officer Dualla describes reports of "system failures" throughout the Fleet and how at least one battlestar loses power when the attack begins, which indicates, that the Cylons use the CNP to damage and, in at least one case, disable capital ships as well.
The CNP was previously received by Galactica, but the program was never loaded into the primary memory of the ship's navigation computer.
Galactica herself is spared from Cylon computer attacks as the CNP is not loaded on any of her computers, nor were her computer systems networked, sparing the ship from any backdoor or cracking attempts.
Unfortunately, Galactica does support a modern squadron of Viper Mark VII fighters, which received the upgrade. As a result, the squadron is massacred by two Raiders on their way back to Caprica.
Lieutenant Felix Gaeta has the CNP source code purged from the mainframe on Baltar's instruction. The program is also retrograded on the flight systems of surviving Mark VII Vipers, Raptors, and civilian ships
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