Atlantia
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The battlestar Atlantia is the flagship of the Colonial Fleet in the Re-imagined Series and the Original Series.
Re-imagined Series
The battlestar Atlantia features integrated command and control systems and Dr. Gaius Baltar's Command Navigation Program (CNP). She is selected by Admiral Nagala as his/her flagship during the Cylon Attack after Fleet Headquarters on Picon is destroyed.
Atlantia herself is soon destroyed over Virgon, a victim of the computer virus spread by the Cylons using the compromised CNP (Miniseries).
It was on Atlantia that William Adama made his 1,000th Viper landing (Act of Contrition). At one point in his career, Chief Petty Officer Galen Tyrol served aboard Atlantia before finally being assigned to Galactica (Resistance).
Atlantia is only mentioned but never seen in the Miniseries.
The Original Series
Atlantia is where the Quorum of Twelve meet in anticipation of the coming treaty between humanity and the Cylons that will bring to an end the Thousand-Yahren War.
Atlantia is destroyed when the treaty rendezvous at Cimtar becomes a trap, along with three of the remaining battlestars of the Colonial fleet, with only Galactica surviving to fend off the Cylons (Saga of a Star World).