The tension between the civilian leadership (Roslyn) and the military leadership (Adama) continues to worsen. It is somewhat reminiscent of the relationship Harry Truman had with General Douglas MacArthur, though Adama has not outright disobeyed an order from the president yet.
Each side of the leadership is presented with several difficult challenges in these episodes. On the military side, one of Adama's top pilots has disappeared after an encounter with a Cylon raider. He dispatches a team to search for the pilot with no success. All the while, the president is getting antsy about the entire fleet being exposed to an imminent Cylon attack if they do not jump to a new location ASAP. Adama tells Roslyn that finding his pilot is a 'military decision' and she tells him that ensuring the survival of her people takes precedence over the life of a single pilot. Adama concedes her point and orders the fleet to prepare to jump.
As a feeling of safety and security begins to permeate the fleet, President Roslyn tells the people that Cylons have managed to infiltrate the fleet and now look human. Adama worries that this will lead to everyone suspecting everyone else, reminiscent of post 9/11 America and the fear that anyone among us could be a terrorist in deep cover.
As episode 9 opens Gaius Baltar is accused of aiding the Cylons to destroy the defense ministry just prior to the attack. The accusation is made by a copy of the number six model onboard Galactica, placing both Commander Adama and President Roslyn in a difficult situation as both have trusted Baltar and given him access to much data and equipment. Baltar maintains his innocence in meetings with both Adama and Roslyn. Adama hopes for Baltar's innocence but Roslyn's 'gut' tells her he is guilty. Baltar asks forgiveness for not wanting to be executed based on her gut feeling.
Episode 10 begins with the discovery of a Cylon saboteur who claims he has planted a nuclear warhead somewhere in the fleet. He is taken into custody and tortured by the military officer in charge of interrogating him, though he refuses to give up any information. President Roslyn arrives and asks what has been learned while expressing disgust over the military tactics. She apologizes for the torture, offers to grant him a pardon in exchange for the information about the bomb and offers peace. He admits the bomb is not real and tells Roslyn that Adama is a Cylon. Roslyn then orders him tossed out into space through the airlock. Roslyn has now taken control and, like Nixon, believes that being president makes her actions legal and beyond question. Justice is now determined by a single judge, President Roslyn.