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Novacek was part of a covert mission from the admiralty of the Colonial Fleet as pilot of a special fighter known as a Stealthstar. The mission was to fly over the Armistice Line for reconnaissance of Cylon activity.
Upon crossing the Line, Bulldog was soon interdicted by an unknown contact. Under fire, his fighter is severely damaged and was spinning out of control.
With two more unknown craft bearing down on him, Commander Adama ordered Novacek's fighter destroyed so as to eliminate any evidence of their incursion into Cylon space. Instead of being killed, however, Novacek ejected a split second before the incoming missile detonated.
Novacek was taken prisoner by the Cylons, where he spent many years in captivity.
Novacek was allowed to escape his imprisonment in a elaborate ruse by the Cylons. Two Raiders in pursuit of Novacek's escape Raider were apparently unable to shoot Bulldog down. As Kara Thrace later discovered, the Cylons deliberately missed, allowing him to escape and bring a measure of terror to the admiral.
Shortly after telling Novacek of Adama's actions that nearly killed Bulldog, Saul Tigh finds Novacek in the process of killing Adama. After stopping him, Tigh harshly berates Novacek for almost giving the Cylons the assassination they wanted.
Later, Novacek is boarding a Raptor, presumably to start a new life on a civilian ship. Before he departs, Admiral Adama presents him a Colonial uniform and assures him he will always have a place as an officer on Galactica (TRS: "Hero").