The battlestar Pegasus, commanded by Admiral Helena Cain, is docked at the shipyards in order to undergo a three-month systems overhaul when the attack occurs. In preparation for the refit, all computer networks are shut down, leaving the battlestar largely unaffected by Cylon-infiltrated Command Navigation Program,CNP. During the attack, Colonel Belzen reports that all computers are down and that the crew must perform all functions manually.

Tethered to its dock, Pegasus is swarmed by Raiders and struck by several missiles. Fuel and ordnance ignite on the battlestar's hangar decks, causing explosions that cause over 700 casualties. Cain orders a hasty departure from the dock, and the ship fires its reverse thrusters and tears itself free from the burning shipyard's umbilicals.

With Pegasus's defenses still down, and two nuclear missile inbound, Cain orders the CIC crew to spin up the FTL drive and to perform a blind jump on her command, despite the risk of reemerging inside a celestial body. The nuclear detonations throughout the shipyard create bursts of electromagnetic radiation that mask the jump and fool the Cylons into believing that the ship is destroyed (TRS: "Pegasus"; "Razor").

Defensively, the structure features vary little and must rely on The Fleet for long term defense, however, the structure includes various Viper hangars, and anti-aircraft turrets along the entire length of the structure.

In the opening moments of the attacks, the Cylons are able to surprise the Colonials by detonating multiple nuclear warheads in range of the shipyards, eliminating the use of DRADIS and blinding both sides involved. The detonations cause moderate damage to the facilities themselves, but leave them intact, indicating they were not directly hit. On fire, and all but defenseless, multiple squadrons of Raiders are then able to jump in and have at the facilities with relative ease, despite being blind. The subsequent assault ultimately destroys the facilities, and various Colonial craft caught in the middle. However, one battlestar was able to escape destruction, break free of her berths, and escape the battle (TRS: "Razor")

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