Other contributors have said "Did scully shoot mulder?" is the same question as "What episode were Mulder and Scully in bed?" If you believe that these are not asking the same thing and should be answered differently, click here
They don't really get together until the last episode of season nine,"The Truth". When they run away together as fugitives. But in season seven mulder kisses scully on new years "Milenium" and he...