Nana Visitor hated the Intendant's rubber figure-hugging outfit. "It didn't breathe at all" claims Visitor, and between takes she had to stand in front of a large fan to prevent her from sweating, as sweat tended to discolor the outfit.
This episode's title, 'Through The Looking Glass'--aside from being from Lewis Carroll's 'Alice in Wonderland'--is also the last line in the previous season's episode in the mirror universe, 'Crossover,' spoken by Major Kira replying to Sisko's inquiry about where she and Bashir were.
This episode was filmed after "Improbable Cause", but before "The Die is Cast" because the decision to make "Improbable Cause" a two-parter came so late in the schedule that "Through the Looking Glass" was already in pre-production.
The raider's corridor, transporter room, and the turbolift, are redresses of the USS Defiant sets, using computer graphics from Star Trek VI: The Undiscovered Country. To make it look different, the lighting department had a harsh red light to make contrast to the bright white lights of "our" universe. The raider's bridge was a redress of the Runabout cockpit which had been re-dressed in the same style several months earlier as the Maquis raider Val Jean in VOY: "Caretaker".
This episode picks up in the mirror universe where Crossover (1994) left off. "Crossover" had itself been something of a sequel to Mirror, Mirror (1967).