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I own nearly all the original shooting scripts from the last two seasons and I have gone through some scripts and plucked out (and scanned) parts of the scripts that prove that the writers were developing a relationship between Doggett and Scully that went beyond their professional partnership.

The Powers That Be Speak

2002 X-Files Yearbook

QUESTION: For a while there we'd had the romantic scenario in which Follmer wanted Reyes who wanted Doggett who wanted Scully. Then the Doggett-wanting-Scully part of the equation seemed to disappear. What happened there?

FRANK SPOTNITZ: I have my own psychoanalysis of Doggett's character and to me the pining for Scully is still there. I believe that John Doggett is incapable of giving himself happiness. I think he punishes himself for the death of his son, blames himself and buries himself in his work and can never do enough to redeem himself in his own mind for his son's death and not finding the killer. To me, it makes perfect psychological sense that he would go after the woman he could never have and that he would be attracted to something that's impossible - that that's what he would allow himself to do with Scully. The woman he should be with and the woman who does understand him and supports him is Monica Reyes. The very fact that she is available to him - and he knows she has feelings for him - is what would keep him from ever responding.

"Doggett/Scully/Mulder Triangle" by Frank Spotnitz
http://biglight.com/blog/doggettscullymulder-triangle/
https://web.archive.org/web/20130917044928/http://biglight.com/blog/doggettscullymulder-triangle/
21 August 2013

CASSIE: Hi Frank, I am hoping that you could elaborate a little bit on this quote from Chris Carter from an interview in 2001:

“From the beginning Doggett has tremendous respect for Scully and I think that respect has blossomed into something else. That was always our intention, that we would have a sort of triangle.” – Chris Carter (Zap2it, November 2001)

Why was there an intention to develop a (love) triangle with Doggett, Scully, and Mulder? As much as I love the idea of a romantic relationship between Doggett and Scully, all fans of the series back during this time knew that no matter what the relationship was always going to end up being Mulder/Scully. I’ve always been very curious about this particular quote and hope that you can provide some insight from a writer’s point of view.

“I got the pretty clear sense that John Doggett was in love with Dana Scully. And of course Dana Scully was in love with Fox Mulder.” – Frank Spotnitz (“DeadAlive” commentary)

Why have John Doggett fall in love with Scully if nothing was going to happen between the two of them? I understand that it was one angle on exploring the Doggett character, but if nothing was specifically done with regards to Doggett’s feelings for her (he never told her how he feels for her, he protected her and became her friend, and someone she could trust, but he never came out and told her how he felt). The Doggett/Scully relationship has always interested me, and I would love to know what triggered the writers into creating this triangle and Doggett falling in love with Scully.

FRANK: Doggett’s affection for Scully was moving to me precisely because we (and he) knew it would never lead to anything. He understood Scully’s heart belonged to Mulder. He would never do anything to challenge that and, in fact, would’ve risked his life to  reunite her with Mulder, if for no other  reason than it’s what Scully so desperately wanted. Doggett’s selflessness added a heroic and somewhat tragic dimension to his character that I found deeply appealing. (Complicating things further was the sense that Monica Reyes had an attraction to Doggett…)

15 August 2001 - TV Guide Interview

“I honestly believe Doggett loves Scully but he doesn’t want to impose himself on her.” - Robert Patrick

Zap2it - November 2001

“From the beginning Doggett has tremendous respect for Scully and I think that respect has blossomed into something else. That was always our intention, that we would have a sort of triangle.” - Chris Carter

Frank Spotnitz Commentary on "DeadAlive" Episode

"I got the pretty clear sense that John Doggett was in love with Dana Scully. And of course Dana Scully was in love with Fox Mulder. So, you sense this heartbreak, you know, she's in love with this guy and he wants to be there for her and he can't be, because her heart's taken by someone else. He so wants to protect her, he so wants to be the one that she's turning to. And that just ain't gonna happen." - Frank Spotnitz

"Inside DSR" by Frank Spotnitz
http://biglight.com/blog/inside-dsr/
https://web.archive.org/web/20100113093510/http://biglight.com/blog/inside-dsr/
12 November 2009

CASSIE: ... Can you give me and other Doggett/Scully fans any inside look at the thought process revolving around creating this attraction that Doggett has for Scully (and possibly she for him)? Why it was done? What attracted Doggett to Scully outside a normal professional manner? How did the actors work with the writers, directors and each other to play out this chemistry and attraction?

FRANK SPOTNITZ: I can’t speak to what Robert and Gillian played under the text, but I can tell you that we spent a lot of time thinking about the nature of Scully’s relationship (romantic or otherwise) with Doggett. From the beginning, we anticipated the audience would miss Mulder and not want to like or accept the Doggett character. We gave full vent to those feelings through Scully (i.e., having her throw water in his face the first time they met). The key to understanding — and coming to love — the Doggett character was in seeing his reaction to her hostility, and to being given the thankless task of “taking Mulder’s place.” Doggett was a decent, honorable man, who always tried to act in accordance with his conscience. I found his situation deeply poignant. He may not have felt any investment in the X-Files assignment, but he clearly came to care for Scully and respect her enormously. He knew her heart was taken by the absent Mulder, so whatever romantic feelings he might have had for her would not be reciprocated. And while she was always perfectly capable of taking care of herself, Doggett couldn’t help feeling somewhat protective of her, as a pregnant woman and then as a new mother.

"Doggett Pursuits"
Ian Spelling Interviewing Robert Patrick
The X-Files Official Magazine - March 2002
Page 14

"Even though Doggett loves Scully, he realized that he was there to protect her, and he didn't intrude on her relationship with Mulder." - Robert Patrick

"A Change Is As Good As A Rest"
Jean Cummings Interviewing Robert Patrick
UK Cult Time #65 Feb 2001
Page 28

"I have thought about the personal life of Doggett and I do ask questions but its not fair to the show to do that. I do think he has a great deal of respect for women and that he really appreicates Scully." - Robert Patrick

Chris Carter's Written Word Per The "Trust No 1" Script

"If Mulder's safety is Doggett's paramount desire, his desire for Scully is always at war with his honor."

("Trust No 1" script, page 36)

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