I don't go for the whole dom/sub idea in fic, but I do know of one story that fits your criteria to a T 'and' is actually a favorite of mine. You definitely have to read Satina's 'Alex Unleashed' -parts one and two (if you haven't already).
http://www.hegalplace.com/satina/mk/alexunleashed.html
http://www.hegalplace.com/satina/mk/alexunleashed2.html
Excellent Sub!Krycek and Dom!Mulder. I just love this fic...and I don't even like that kind of relationship. But I must admit - I prefer the idea of Mulder as the dom...I'm so sick of Sub!Mulder I could cry...
Nikita
www.koukla.net/nikita_slash