By the time this episode aired, the character of Gul Dukat had become exceptionally popular among fans of the show, far more popular than any of the writers had ever intended. This was primarily attributed to Marc Alaimo's superbly charismatic performances as Dukat.
This episode originally ended with Dukat saying to Sisko, "You too will learn what it's like to lose a child," but the writers abandoned this idea because it was too specific and it locked them into one path in terms of where to next take the character.
Two of the ships in the search party, the Constellation and the Defiant, are named after previously destroyed ships from Kirk's time. The Constellation was destroyed in The Doomsday Machine (1967) and the Defiant was destroyed in The Tholian Web (1968) (where the mirror universe crew of the NX-01 Enterprise steal it).
This episode references an attempt on Dukat's life on Terok Nor within the first month of his administration where someone placed a bomb outside his quarters. This might well be the attempt on the life of Kira Meru as seen in Wrongs Darker than Death or Night (1998).
This is the second DS9 episode in a row to use a light redress of the Star Trek: Voyager (1995) brig set. It appears as the brig of the USS Honshu after appearing as a brig on a Federation starbase in the previous The Magnificent Ferengi (1998).