I have to disagree about Kes being almost invisible in the last episodes of season 3. She did have a certain amount of screen time in the episodes "Real Life", "Displaced" and most of all "Scorpion #1". In fact, her appearances in "Before And After" and "Scorpion" gave me the impression that she would play a more important role in the future seasons of Voyager.
Now, if they planned to dump her early on, they had the opportunity to do so in "Darkling" but as we saw, Kes did choose to stay on the ship with her friends and colleagues. Not to mention that if there had been a plan back in season 3 to dump the character in the beginning of season 4, I'm sure that the producers and writers should have come up with that as an official excuse when people started to question their original statement that "Jennifer left of her own free will".
As for "that episode in season 6" and their reason for coming up with it, I still think that it was a reply to those fans who committed a blasphemy by trying to persuade the "gods" to bring back Kes as a regular character in season 6. I still see no reason at all for bringing back a character which they had made everything possible to wipe out from the history of Voyager and from the minds of the fans.
What I know and have heard about from some sources, the letter campaign was noted among the "gods" of the Star Trek Universe. So those "gods" had two options:
1. Bring back the character as a regular in season 7 (if Jennifer had accepted to do it).
2. Totally ignore the wishes of the Kes fans and continue as before.
Option 2 would have been the logical choice if they hadn't noticed the campaign or simply had chosen to ignore it.
Instead they went for option 3, to bring back the character only to destroy, humiliate and finnaly kill of the character which was their original plan and by doing so showing a finger to those obnoxious fans who had commited blasphemy by question their former decision to kick out the character and even worse, tried to tell them what to do.
If they wanted drama and high ratings, there were a lot of other things they could have done. Henry Starling returning from the future, a horror episode with Suspiria or simply play safe with their beloved "TNG card" by bringing in Q, Riker, Picard, or a resurrected Tasha Yar or something like that. Or maybe Captain Kirk himself from an alternate timeline. Something like that could have given Voyager a shot in the arm and rasied interest outside the Voyager fanbase for a show which had been going down in ratings and interest since the temporal raise when Seven was introduced.
Did they really think that Voyager fans in general and Kes fans in particular would like that episode? No, I don't think that they were that stupid. They did know exactly what they were doing.
At that point they had more and less given up on Voyager and was planning ahead for their new project Enterprise where they should show the world how TOS really should have been made from the beginning. They just let Voyager run its course and finished the race by showing the finger to another Voyager fanbase, the even bigger J/C fanbase by throwing the Chakotay-Seven romance in their faces.
Lynx,
As far as my statement about the last five episodes, it's not really a contention, it's much closer to being a fact. Check out her line counts in Chakoteya. I'm not saying she was totally absent from the Doc's reconsideration of his happy home, but there's no doubt that B'Elanna was the driving force. Displaced? Really? 1 line. Period. And if you choose to watch it again sometime, you will notice exactly what I'm referring to about the apparent blocking of her being even seen clearly, let alone heard from again. As for Scorpion 1, how did her representation differ from what we saw in Part 2, other than just being the introduction that tells us that we are about to see episodes in which her raison d'etre is to once again have progressively advanced psychic powers that will allow her to be the Cassandra that sounds the warning klakon about the Undine. If no other aspects of her character that we were used to viewing, are shown in Part 2, at which time it's been established that the decision for Lien to get the chop had been made, what makes you think that the intentionality of her role in Part 1, realistically implied a greater role in the show in the future, let alone that she had a future? As I've said, that the People spoke up for Wang may really have been the coup de grace. Yes, Kim was tantalizingly near death in 1, but wasn't that simply the mechanism to show how to develop the means to defeat the galaxy killers, aside from the fact that he was back in the pink (well except for his negligence in using a hankie before returning to duty)
before 1 ended, not resurrected just in the nick of time in 2, that
would have factored in the immense power of his one week newsstand notoriety?What I'm saying is that my growing suspicion that Lien was
likely to have been the one decided to be jettisoned before 2, seems more plausible based on the lack of exposure in those final episodes, and that her centrality in Darkling and B&A can, I think, be readily seen as prefigurements of that decision being at least contemplated earlier in the season (no. not early on), by virtue of the content of those episodes and the implications that they conveyed. I seriously doubt that the determination had been made at the time of Darkling, so contending that she could have just as easily disembarked then, doesn't really stand up to scrutiny I think, aside from which, it would have been rather awkward for her to leave about three quarters of the way through the season. Also, I don't believe that TPTB would have been inclined to pay Lien for seven episodes worth of salary for no work at all. Finally, what really is the basis for all your wrangling over the wording of her release? I hardly think they would admit that they plainly didn't want her around any more or that their writers couldn't have done more effective work highlighting the character, if that was their intention (although of course it should have been). She wasn't fired, she simply wasn't renewed. However, official explanations can be maintained to have played Ring around the Rosie with that fact, seems pretty irrelevant and a matter of semantics that could be jerked around with, however it was desired.
As to your positing of perceived options that the show runners had to decide between, or create a hybrid, because it was forced on them by this groundswell of fans with pitchforks, well I'd like to see the sources you cite of a sizable letter campaign that got in the face of said villains. I have no doubt that most, if not all , Kes sites that were extant at the time, would have been agitating for such an outpouring of deeply felt correspondence demanding a return. But, realistically after all that time, how many disgruntled Kes fans are we talking about? I believe that were far more audience members just plain disgruntled with the show in general, than for the reason you suggest. Also, why would such a campaign that sought a mass demonstration not have happened far earlier, such as just after the character was expurgated? Wouldn't it seem logical that developing a critical mass would have been much more plausible right away, than two plus years later? This notion of the suits being faced with an issue like this that had to be dealt with, I'm sorry but it seems much more like wishful thinking, than something at all tenable, again absent anything quantifiable that one can produce to give it any credence. My sense is that presenting anything from the sources you refer to, would be a pretty quixotic search at this point, but I certainly would be more than a little interested to view it.
I don't think you've alleged anything that would counter what I thought was the likely provenance of Fury, which again, is hardly a novel, or perhaps more importantly, very difficult concept to forward to easily fill the demands of an episode, at a specific time, when perhaps the writers weren't coming up with anything particularly compelling otherwise. I really don't find your alternate oldie but goodie recommendations, to be ideas that would set the world on fire, or as Chakotay struggled so to do, set a fire at all. Picard and Riker? Wouldn't they tend to dominate the scenery, making our nominal heroes rather scarce? We got that brilliant idea some years later in a rather more significant episode. I don't think having had a precursor of that bilge would have played out to the advantage of the Voyager cast any more successfully. Another Q? Don't a lot of folks think that he'd been worn down to mediocre histrionics by his last appearance on the show? Henry Starling? I think the amount of plundering that had actually been shown was quite sufficient to make the idea of another appearance less than scintillating. Now, Rain Robinson somehow being worked in again, that's another story, but....you didn't mention it.

Kirk? Would Shatner really have been particularly motivated to show up in what was widely perceived to be a wan, deracinated disappointment? I like Suspiria, but really only in a totally redone series finale, one in which Kes would definitely appear.
I won't point to it as a great example of Trek dramaturgy, but I don't think one has to fish around quite so strenuously to find the premise plausible, and she did get to go home at the end, alive and once again aware of the reality of what happened before her grand adventure, that simply didn't work out as she so hoped and anticipated it would when it began. Also, in the name of accuracy, while Kes didn't exactly trip off the tongues of characters frequently after she left, I believe she wasn't absolutely wiped from the audience's memory, being mentioned in two episodes afterwards, I believe. (Voyager Conspiracy and another I can't recall at the moment).
Not that it's hard to give him credit for that, but to me it seems like that's what anyone in a loving relationship would do....well SHOULD do
While I'm about as far from your opinion of the abilities of Jennifer Lien and how she used them to create one of the singular characters (not major, mind you, though could have been) in not only the series, but the canon, I do give you many kudos for what, plainly should be the verity in a relationship constituted of, and meant for the deepest essence, that can exist between two people, clearly putting aside as irrelevant, peculiar quirks of the couple's divergent physiognomy, only in play for a very short time anyway. Such a union deserves the full respect that allowing it to play out to the end, with the same commitment that it began with, is a core value that all of us would be better off seeing more of in our own world!!!
I wasn't talking about when Tom was married to Kes. She was already the mother of his baby girl and everything, so naturally, her status was instantly elevated to where no matter what else happened between them, ever after, she'd always have that over him. Tom owed Kes everything ... everything. But when Kes started to age out of the relationship to where she's ... like ... old and decrepit and Tom's still young and virile ... what's it all about? How could he stay married to her? He does! Of course, we see that in the final thing. But ...
Yeah, in my 'head canon' if you like, Tom & Kes had stopped being intimate for a quite while, by that point. He should have, if not divorced her, outright ... at least "separated" from Kes. And at the same time always being there, for her. When she needed him, he'd be there, like Johnny on the Spot. Anytime. For anything. He'd be there. That's what I was really getting at, not so much loving her up, when they were kind of equal in the relationship. I was talking more about after Kes had gotten too old for Tom. She'd stopped becoming his wife and became his granny ... what to do? You know? What to do ...
Of all people, you probably know that episode as well as one can. Again, Kes looked almost exactly the same as when Linnis came into the world, only slightly more than six months before the demise that would have befallen her, at exactly the natural life span (at least of non-enhanced or perhaps pre-Nacene contact Ocampans) that was allotted her. If her journey hadn't begun when it did, is there any reason to presume that in her last year or two she wouldn't have appeared as was the case when she
did receive that treatment in her return to the present day timeline? So 6-8 months before natural death, still getting some. A month or two before said death, when she was still working, quite an attractive if nominally middle aged woman. I don't see why Tom's drive wouldn't still be on autopilot at that point. Last few weeks to month, all right she's definitely significantly older looking, but hardly one of the crones from Macbeth. Gentle physical companionship and reassurance would still have been in order, but for the fact that her pilot light was out and her perception would have been being felt up, albeit benignly, by a total stranger. Probably not a pleasant experience for either of them. But that's all of maybe a month. Good god man, you really don't think Tom was capable of such an adjustment for someone who saved him, and in return, he wanted and desired more than anything else to have his world revolve around? Finally, as said above, without temporal shenanigans entering into play, Kes back to her most beautiful for most of that gifted life extension. Definitely getting some.
In any case, I just don't see you have made any kind of convincing argument, even if Tom was the type of individual so callously hung up on appearances(which he wasn't) to the person whom he pledged an existence to be lived to the end, which he obviously knew what the parameters were, from the beginning.