In the episode "The Red and the Black", Krycek kisses Mulder on the cheek.
This scene always had an improvised feel to me.
Was the kiss scripted or was it improvised on the spot?
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According to the DVD commentary for the 'The Red and the Black' (by the show's writer and Director, Chris Carter) the kiss was added at the suggestion of the actor Nicholas Lea. The implication is that it wasn't originally scripted but neither was it wholly improvised:
[Krycek mentions the alien rebel, currently being held captive. He says that if that alien dies, so does the resistance. Krycek kisses Mulder.]
Chris Carter: I think that was Nick Lea's idea, I think he always secretly wanted to kiss David Duchovny.