Late in the writing process, it was realized that the "opera house" sequence could be shown to parallel the ongoing battle on Galatica. Anders' hybrid tank was set up on the CIC balcony, and it was arranged that the other four Cylons be near him, so that the "final five" could be posed in a manner similar to that shown in the opera house dream. In order for the actors to be visible at the appropriate angle, however, a safety railing had to be removed from the CIC balcony.
In the final draft script, Chief Tyrol's final lines mentioned him moving to an island off the northern continent. At the request of Aaron Douglas, this line was expanded to include a mention of the "highlands". Ronald D. Moore, in the episode commentary, confirms that this line is intended to imply that Tyrol is the founder of Scotland.
The original cut (of all three parts) of the series finale ran over four hours long.
Kara Trace quotes directly from the song, "All Along the Watchtower" as she's inputting the coordinates for Earth into the FTL drive: "There must be some kind of way out of here". The song's notes are an integral part of finding a new home for humanity and the ultimate conclusion of the show.
The deleted scenes for this episode include two scenes where Tory Foster and Boomer are being "planted" into human society, after having their memories altered. Ronald D. Moore, in the commentary, indicates that these scenes will probably be integrated into Battlestar Galactica: The Plan (2009).
Ronald D. Moore: man at the New York City newsstand reading about the discovery of Hera Agathon's skeleton while 'Six' and 'Baltar' comment about it behind him.