This is the first episode in which the Bajoran Occupational Government is mentioned. It was previously implied that the Cardassians simply eliminated the Bajoran government altogether during the Occupation of Bajor. The Ilvian Proclamation, which sentenced all collaborators to exile, is also revealed.
According to the Star Trek: Deep Space Nine Companion, there are several Watergate parallels in this one: for example, when Quark helps Kira bypass the security lockouts, and the Prylar Bek character, whom the Companion claims is based on John Dean.
The visible tension between Winn and the crew of DS9 is left over from Winn's attempt to stop Keiko O'Brien teaching secular science to Bajoran schoolchildren. During a visit to the station, Winn coerced a Bajoran engineer to try to kill Vedek Bareil, who opposed Winn's way of thinking and threatened her popular support. However, as there was no evidence to prove her involvement, she was never indicted.
Gary Holland's original idea involved an elderly male Bajoran who had been living on Cardassia for many years and who wanted to return home to Bajor. It is thought this Bajoran has some kind of dark secret, and Kira is assigned to find out what it is. At first, it seems the secret may be the man murderered Kira's father. It later transpires the actual murderer is in fact his daughter, and he is covering up for her.