Colonial Defense Mainframe
From Battlestar Wiki, the free, open content Battlestar Galactica encyclopedia and episode guide
The Colonial Defense Mainframe was the high-security central computer where it's presumed all Colonial Fleet data, logistics, strategies, and software are managed, stored, and tested. It is presumed that the Defense Mainframe resided in, or was accessible from Caprica City.
Two years prior to the events in the Miniseries, scientist Gaius Baltar allowed a fellow programmer and love interest to aid him in completing the Command Navigation Program, an avionics operating system for use on most Colonial ships, fighters, and some civilian ships. The woman, an experienced programmer herself, rewrote many of the CNP's algorthms and other programming. The CNP was distributed as part of a fleet software upgrade a short time later.
Baltar discovers later that his love interest and collaborator is a Cylon agent, model Number Six, who used Baltar to gain access not only to the CNP, but to the Colonial Fleet's "communications frequencies, deployment schedules, unlimited access to every database." As a result, his Command Navigation Program contained a backdoor that allows the Cylon Raiders and basestars to send commands to disable any CNP-equipped Colonial ship, from fighters to battlestars, leaving them defenseless.
Galactica's computer systems were never networked, nor was the CNP installed to any of its subsystems. As a result, Galactica survives while almost all of her sister ships meet their demise in the Fall of the Twelve Colonies. Unknown to Galactica at the time, the battlestar Pegasus survives by virtue of having its computer systems offline while in space dock during the Cylon assault.
According to Shelly Godfrey, the Defense Mainframe was destroyed by an explosive device, ostensibly placed there by Gaius Baltar, moments before the Cylon Attack (Six Degrees of Separation). The charge is later dropped when an investigation reveals that Baltar's image had been falsified in the recording from Godfrey.
In the last episode of the series Daybreak, Part II it was revealed that Baltar deliberately with prior calculation provided the information of the Colonial Defense Mainframe to his girlfriend Caprica Six who he knew would give the information to her "Employers". At the time he still did not know Caprica Six was a Cylon, and certainly didn't know that his action would result tin the deaths of billions of people but did actively conspire to commit espionage. Prior to this revelation it was thought by implication or inference that he gave her the information out of a narcissistic need to impress her. In either case he implies he did it for love for her.