But an entire episode was also made about how there were an infinity of timelines.
Yeah... well, that one seems a bit separate from the others. In TOS, Trek had already established a "tradition" that this universe could have parallels in more than one sense or way. First, a matter/antimatter parallel. Then a sort of evil/good parallel (which is why Mirror Mirror doesn't bear up under questioning)... So I guess this universe has one-on-one parallels, plus multiverse parallels that I doubt the previous ones (AF, MM) were any part of. Time splinter sub-universes without separate beginnings may be another, or Parallels may have been that.
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Back to Endgame...
Answering a few earlier posts... Erasing lives before they happen is NOT murder. Because they now never lived. You can't murder people who didn't exist in the first place.
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On Endgame (I really groaned at that overused title!) ... presumably older Janeway knew of all sorts of people and future developments that we aren't privy to. All that should have been very real to her. So it should have bothered her, wiping all that out... but maybe she has informed knowledge that we don't, that lets her know her actions won't damage history much.
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A lot of what Trek has been about over the decades is that sometimes you have to break the rules. A large group within fandom seem to be dedicated rules followers. Nothing is absolute right or wrong.
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I see older KJ's actions as coming out of a failing, a mis-step, on the part of older Janeway... which younger Janeway helped her to resolve. Presumably when Janeway reaches that age again, she'll have a better perspective on time travel.
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Let characters be human and have flaws. As you watch Janeway doing something questionable, ask yourself, "Wouldn't I be tempted to do the same thing?" It's easy to sit in a comfortable chair watching TV, not facing these challenges ourselves, and judge. Good drama gets us to ask ourselves these questions, about our own weaknesses. They are attempting to do that.
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Upholding a high-minded, abstract ethical point like "never interfere no matter what" can even look a bit cowardly, when faced with deaths and suffering right in front of you, that you can prevent. I would need to be reminded which specific 100 lives old Janeway is wiping out... but all time travel plays with potentially countless lives.
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On time travel altering things... I see the Temporal Prime Directive as a giant temporary band aid on a huge issue we didn't know how to address. It didn't mean Starfleet or the Federation has determined that it's "wrong" or inherently destructive. They merely went, "AAAAA!!!", and slapped a prohibition on it. It's too risky in vague ways we can't understand yet.
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Also, every day for Voyager, Starfleet, and all sentient beings was/is an exercise in improvising solutions, and not knowing what the results will be. Time travel is therefore not necessarily all that different.