All series after TOS had their opportunities to incorporate or wrap up a loose end made from TOS' stories, or a DS9 arc wrapping up a loose end from a TNG story. I have always felt that Section 31 could have played a much bigger part than just the shadowy black ops group that it was portrayed as. Watching that arc, I wished very hard that a fleet of Federation ships, made out of Nuetronium, would have grouped at DS9 and they would have led the invasion into Cardassian space. Remember, I'm talking about a loose end. The Doomsday Machine was stopped and never seen again, so why not have the Feds come and haul it somewhere for study and eventually used for their ends?