The Section 31 miniseries foreshadowed an end-of-Section-31 pitch that never ended up being made.
Or which hasn't happened yet.
The beginning of The Sundered makes explicit references to Forged In Fire, which was published 5 years later.
Yeah, but was that Marco's doing or Martin and Mangel's?
I doubt that the Section 31 story will be gotten back to anytime soon. Mike and I had really started setting up the idea for a big hardcover cross-over, which is why Rogue had many of the ending threads it had, and other books followed suit. Other projects kept getting put in the way, including A Time To, and then Titan, and then... and every time we brought up Section 31, it got pushed back again. Other things just took the lead, and now, it would take far too much time to get back to that story in today's continuity.
And I don't recall the explicit references with Sundered and FiF, but Mike and I did make a LOT of effort to tie a lot of our books together by threads... especially when they were of the same ship. We had done early work on FiF prior to The Sundered, as I recall (FiF had a very long gestation period).
When working out the initial plot - if he wanted certain things - Marco would more often give us very specific story beats to hit, or end results for characters or situations, but how we got to them was up to us in the plotting stages. Sometimes we got almost no story beats ahead, other times (such as the DS9 books) we got a lot of them.
But as a for instance, in Worlds of DS9 Trill, I recall that our main story beats that Marco wanted were: (a) it had to take place on Trill; (b) it had to address the history of the Trill; and (c) it had to feature the dissolution of Bashir and Ezri's relationship. I believe the tie-in to the parasites was Mike's idea (as was much of the Trill history), and I think I came up with the terrorism subplots and the "end of joining" ending that was a real game-changer. Of course both Mike and I contributed parts of all of the ideas, and then it was submitted to Marco, who worked with us to better things he didn't think worked.
And I agree that Marco seemed to like "hopeful-but-melancholy" endings and stories. I do as well, much of the time, as it gives more of a continuation for character development. "Happily Ever After" or "He/She's Dead," don't leave a lot of interesting avenues to travel on for the future...