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In other words...
I love you

These quotes are taken from various episodes...

SCULLY: Not that, uh, my only joy in life is proving you wrong.
MULDER: When have you proven me wrong?
SCULLY: Well... Why else would you want me out there with you?
MULDER: You didn't want to be there? (pause) Oh, that's, um... That's self-righteous and... narcissistic of me to say, isn't it?
SCULLY: No, I mean... Maybe I did want to be out there with you.

--How the Ghosts Stole Christmas, Season 6


SCULLY: Well, it seems to me that the best relationships-- the ones that last-- are frequently the ones that are rooted in friendship. You know, one day you look at the person and you see something more than you did the night before. Like a switch has been flicked somewhere. And the person who was just a friend is... suddenly the only person you can ever imagine yourself with.

--Rain King, Season 6


MULDER: In four years I have shared my partner's passionate search for the truth, and if my part has been a deception, I have never seen her integrity waver or her honor compromised, but now I ask her to lie, to the people lying to us, a dangerous lie to find the truth. --Redux, Season 5


Scully: Mulder, if I can save you, let me. Let me at least give some meaning to what's happened to me.

--Redux II, Season 5


Mulder: Scully, I can't let you take the blame. Because of your brother, because of your mother, and because I couldn't live with it. To live the lie, you have to believe it. Like these men who decieve us, who gave you this disease. We all have our faith, and mine is in the truth.
Scully: Then why'd you come here if you'd already made up your mind?
Mulder: Because I knew you'd talk me out of it if I was making a mistake.
Scully: You'll be in my prayers.

--Redux 2, Season 5


SCULLY: I feel these words as if their meaning were weight being lifted from me, knowing that you will read them and share my burden, as I have come to trust no other. That you should know my heart, look into it, finding there the memory and experience that belong to you, that are you, is a comfort to me now as I feel the tethers loose and the prospects darken for the continuance of a journey that began not so long ago, and which began again with a faith shakened and strengthened by your convictions. If not for which I might never have been so strong now as I cross to face you and look at you incomplete, hoping that you will forgive me for not making the rest of the journey with you.

--Memento Mori, Season 4


SCULLY: Mulder, I hope that in these terms you might know it and know me and accept this stranger some may recognize but cannot ever completely cast out. And if the darkness should have swallowed me as you read this, you must never think there was the possibility of some secret intervention, something you might have done. And though we've traveled far together, this last distance must necessarily be traveled alone.

--Memento Mori, Season 4


SCULLY: I have not written to you in the last 24 hours because the treatment has weakened my spirit as well as my body. Mulder, it's difficult to describe to you the fear of facing an enemy which I can neither conquer nor escape. Penny Northern has taken a downturn. I now look at her with a respect that can only come from one who is about to walk the same dark path. Seeing her I can't help but see myself in a month or a year. I pray that I have her courage to face this journey. Mulder, I feel you close though I know you are now pursuing your own path. For that I am grateful, more than I could ever express. I need to know you're out there if I am ever to see through this.

--Memento Mori, Season 4


MULDER: Hey, Scully.
SCULLY: Yes, Mulder?
MULDER: I love you.

--Triangle, Season 6


Many thanks to Tiny Dancer's X-Files Transcripts and The X-Files Haven for the FBI's Most Unwanted