How Trip Tucker Died and Got Better
The ENTERPRISE novel, LAST FULL MEASURE, released after the cancellation, has a framing sequence in which a five year old James Kirk is visiting the Starfleet War Memorial and meets an old man who shares little Jimmy's reverence for Starfleet's ideals. We then go into the main story which is set during Season 3 of ENTERPRISE and is an untold adventure of Enterprise investigating the Xindi threat. When we return to the framing sequence at the end, the narration reveals that the old man is Trip Tucker, decades older than he was in his reported death in "These are the Voyages."
With the sequel, THE GOOD THAT MEN DO, a framing sequence has Jake and Nog hanging out and doing some research for one of Jake's books. Jake has stumbled across a strange cover-up; historical records have been altered with regards to the build-up to the Romulan War and the intial formation for the Coalition of Planets. Jake and Nog realize that all this has been done to falsify the death of Charles Tucker III.
We go back to the events of "These Are The Voyages" where we get the full story that exposes the holodeck simulation as a fraud. Tucker is recruited by Section 31 to prevent a Romulan attack and is forced to fake his own death to go undercover. THE GOOD THAT MEN DO also highlights how, when leading up to Trip's death scene in the aired episode, Trip winked at Archer and Archer smiled and then buried the smile, and then Archer gave Phlox a conspiratorial look.
I have no idea if the actors or directors or whoever were deliberately seeding the idea that this entire situation was a ruse or if the editors chose a take where the performers broke character or if Jolene Blalock got everyone high before filming, but it's onscreen and novelists Andy Mangels and Michael Martin seized on that. Good.
Trip is separated from his crewmates and becomes a pivotal figure in the ongoing ENTERPRISE novel series as the Romulan War alluded to in the original TREK becomes the center of the story.
I would now like Slider_Quinn21 to chime in and say these novels aren't canon.
With regards to Roddenberry's vision -- what stands out to me is that the original STAR TREK had Kirk and McCoy regularly blowing up and arguing and Kirk was a man of sexual appetites. Spock was certainly a breakout character with his value system, impeccable morality and cool, scientific personality and he contrasted well with his more human co-stars.
Then in the 70s, Spock's status as the breakout character of the show caused Roddenberry to take the view that Spock's philosophies were completely universal for every single character in TREK. Roddenberry seemed to forget that Kirk and McCoy and Scotty and Sulu and Chekov hadn't been anything like Spock. And while after the first TREK film, Roddenberry was relieved of control, he was responsible for THE NEXT GENERATION's first two seasons and its clumsy, witless, lecturing tone.
Writers like Ronald D. Moore and Michael Piller worked within the restrictions. Piller wrote a script where a boy grieves his dead mother. Roddenberry rejected it; people in the 24th century (or Spock) wouldn't grieve death. Piller rewrote it so that the aliens who accidentally killed mom try to push the kid into grief in an effort to atone for their error and his loss. This was accepted.
DS9 found other ways to be get around the limitations, mostly by indicating that the perfect world Roddenberry imagined was merely the Federation and by situating DS9 in proximity to Bajor and Cardassia, DS9 could bypass Roddenberry's restrictions while respecting their values.
They did introduce Section 31, the Federation's black-ops assassins. However, they also made sure to leave themselves some wiggle room by noting that Section 31 is unsanctioned with no official status and could arguably be considered a rogue organization that isn't part of Gene Roddenberry's perfect Federation.
If Ronald D. Moore and Ira Steven Behr had not felt a duty to be follow the letter of the law laid down by the original creator, I imagine they would have gone so far as to say that Gene's values were just that -- values -- existing in contast to a more complicated reality. But as STAR TREK had really put forth an ideal world as an actual reality, I think they felt it best to stick with that for the Federation while noting that there were lots of exceptions in the margins and outside the UNFP -- and they could do morally ambiguous worlds on their own shows.
And I think that's the best route because we should not make STAR TREK more like our world. We should make our world more like STAR TREK. But we also shouldn't be so reverential to a very flawed TV creator that we don't dare step outside his many arbitrary and asinine limitations, and then like Berman and Braga, lose any sense of how to tell a story with conflict, drama, risk, meaning and something to say.