Througout many of the episodes, Scully's apartment numbers are usually in the higher numbered range (I've seen it in the 400's). However, in "Duane Barry," Scully was kidnapped through her ground floor window.
actually in the majority of the episodes, mulder's apartment number is 42 and scully's is 5. it does change a lot (a lot of the hotel numbers are higher, and sometimes her apartment number even changes) but usually her number is 5.
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