One of the most debated aspects of the show is Shepherd Book's secret past. He holds some sort of priority status within the Alliance (demonstrated in "Safe"), and on numerous occasions he demonstrates a depth of knowledge in a number of fields, including space travel, firearms, and criminal activity.

In the fourteenth and final episode of Firefly, "Objects in space", Simon berates the bounty hunter, Jubal Early, for assaulting Book, a Shepherd. Early only replies mysteriously, "That ain't a Shepherd." Early's implication that he knows something about Book's history is never explained. Earlier in the same episode, a similarly inscrutable insight occurs when River Tam reads Book's mind: "I don't give half a hump if you're innocent or not! So where does that put you?" This cryptic thought is uncharacteristic of Book's normally kindly demeanour, again hinting tantalizingly at an underlying duality.

Though Book himself often hints at a dark past, he refuses to discuss it openly. When asked by Mal if he would like to explain the preferential treatment the Alliance gives him in "Safe", he responds, "I surely would, and maybe someday I will." However, in Serenity, Book seems more reticent to share. After Book describes the methods and mentality of an operative of the Parliament, Mal presses him for some explanation of his knowledge, but receives none.

The truth about Book's past may never be known, as Book perishes in Serenity, without ever revealing his secret.