President Roslin's fears that Commander Adama is a Cylon are stoked when she learns he's making secret wireless calls to other ships. Then, to make things worse, a single Cylon raider appears near the Galactica and begins acting strangely after being damaged in battle.

Now on board Galactica, Baltar faces charges of treason. He contemplates suicide with the help of Number Six. Questions remain about his true identity. Is he a Cylon or isn't he? Apollo shows off the new drinking establishment on Galactica, Joe's Bar, to Tyrol. Apollo thinks about Kara and wonders whether his marriage to Dee is worth saving.

Gaius Baltar sets off a debate on religious freedom when he promotes his belief in a single God.

Ellen escapes from Cavil only to face a momentous choice regarding the 13th Tribe and the Final Five Cylons.

The rebel Cylons and the Colonial humans react to Hera's kidnapping while the physical condition of the Galactica continues to deteriorate.

The first Cylon war has been raging for 10 years and a young Ensign William Adama joins the fleet. He's disappointed not to be assigned to a fighter but to a freighter. His co-pilot, Lt. Coker Fasjovic, isn't too keen on having a rookie flying his aircraft as he has only a short time before he again becomes a civilian. Their cargo is a civilian scientist, Dr. Becca Kelly, but they no sooner leave than she has new orders for them and a new destination. She is less than forthcoming about just what her secret mission is but Adama is keen, particularly as it involves going into Cylon controlled space. Nothing is as it seems however.