#all things

David Duchovny began his battle with FOX while filming Season 7, definitively declaring he was leaving the show because of a list of (valid) grievances (pay and burnout primarily.) He, the writers, the crew, the actors, the press, the fans all knew he was planning to bail after the finale wrapped-- which was why Spotnitz and Carter began prepping for Scully's surprise pregnancy as early as Amor Fati (e.g. the family planning book hiding in the basement, the boy on the beach referencing the UFO in Africa, CC and Spotnitz writing all things with Gillian Anderson, and Spotnitz confirming all things's opener pointed to William's conception.)

The creed of the show (that Glen Morgan voiced in 2024) was, "Whenever we go back to being at the FOX commissary-- or wherever it was that we were thinking about this stuff-- we had two rules: if Scully ever saw an alien, or they ever kissed, the show was over." However, with DD leaving-- and the old formula, by necessity, changing-- Carter and Spotnitz set up Scully's pregnancy in Requiem to-- as they hoped-- launch a second X-Files movie (which Duchovny, and Anderson, already expressed interest in doing.) And after John Shiban convinced CC to include a New Year's kiss, all bets were off. To quote Wikipedia (because I'm lazy) quoting Marc Shapiro's All Things: The Official Guide to The X-Files: John Shiban developed the idea for a Mulder–Scully kiss, which was described by series creator Chris Carter as a "present for the fans." Shiban noted that the episode's kiss felt like "the logical culmination of their relationship. They had been heading toward the kiss for years". Gillian Anderson later explained that, "David [Duchovny] and I knew the kiss was coming. [...] I felt the editors of that episode milked it in a very effective way." In order to create the atmosphere of the scene, specialized camera angles were used and everything was slowed down to make the scene last longer.

So, Mulder and Scully kissed, and the game changed. The lead writers penned Sein und Zeit and Closure-- a resolution to Mulder's arc-- and collaborated on all things-- a resolution to Scully's arc; and, with Gillian's permission, slipped in a scene confirming the characters' relationship.

Those points have been confirmed; but there are, of course, more points on the "season of secret sex" graph to draw a straight line.

For one thing, the props department sprinkled clues everywhere: an extra toothbrush on Mulder's sink in Orison (thanks to anon and @b0oker18 for noticing), Scully's supplies tucked away in Mulder's bathroom in all things (thanks @unremarkablehouse and @touchstoneaf)-- touches which delicately establish a relationship in full swing. And, as every person working on every level of 1013 attested (on both runs of the show, and the movies), nothing ever happened on-set without CC knowing or approving it.

Scully and Mulder were given more allowances that season, too-- or David Duchovny and Gillian Anderson just... stopped caring about the "will they, won't they?" after Millennium's decisive "they did." Mulder grinning at Scully's arrival and teasing her over her jealousy, Scully territorially bumping into him and playing with his tie, and both of them arriving late for work together in Rush (here); Scully suggestively hinting they wrap up the case (here) and stating she loves baseball now, too (here), in The Goldberg Variation; Mulder having a second toothbrush on his sink (here) in Orison; Scully staying the night with Mulder and not flinching when Skinner catches them (here and here) in Sein und Zeit; Mulder teasing about Catholic girls and snake handling (here) in Signs & Wonders; Scully's beauty tools residing in Mulder's bathroom (here) in all things-- those instances (and more) all highlight the glaringly obvious next step in the agents' partnership. Not to mention Carter's own flirty episode, Fight Club (here.)

I don't know, man, but there's a difference in DD and GA's acting pre-and post-Millennium. It's palpable. They knew the jig was up.

I've touched on Season 7's relationship here, if you're curious.

Also, for the fun of it, I'm including some speculations about the Season of Secret Sex (or all things) that I came across in my archive dive, courtesy of @agent-troi (here) and @deathsbestgirl (here) and @nachosncheezies (here) and @numinousmysteries (here) and @b0oker18 (here) and @thursdayinspace (here.)