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What mysteries of Star Trek would you like to see solved (and, if you want to say it, how would you solve them)?

How they represent themselves is irrelevant to how the story depicts them to the audience.

Only Section 31 was ever cast in the antagonist role.

Not saying you're wrong, but until we have an episode where the Aegis (where did that come from?) is the villain, we only have evidence of them being on the side of "right".
Stipulated.
 
Aegis is what Gary Seven's people were called in he now defunct "Litverse" novel continuity. It's not canon at all.
 
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Stipulated.
I seem to remember Aegis going genocidal in one of the comics, but of course that’s non-canon.

Actually, have they ever been referred to onscreen as Aegis? Because if not, it’s really just the Travelers and their agents, isn’t it?
 
Either way, to assume the Aegis-related folks must be 'good' because we only see them perform deeds we agree with is just as fraught as assuming S31 must be 'bad' because we only see them when they screw up or perform deeds we disagree with.

We could pick and choose certain Trek episodes and easily lead someone to conclude that Starfleet is horrible.
 
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Ther are many things in Star Trek that are not explained. Origin of Borg. Who the Jem;Hadar were before the Founders modified them. What is the origin of Q. Barash's species. Where did all these strtange entities from TOS came from It woul take a lot to list all of it. I ask you: what star Trek mystery would you liek to see solved. And, if you want, tell is how would you solve it (in as many details, or as less, as you want).
Actually, I don't want ANY of these solved! Because they aren't really "mysteries" in my opinion. There are just "origin stories", like "Where does Han Solo come from?".

"Some species experimented with Cybernetics & accidentally created the Borg" is IMO a much stronger origin story than "Section 31's Control traveled back in time and infected V'Ger to destroy the mirror universe, but mind-melded with Burnham, which then created the Borg" or something like that, because these types of "origin" stories somehow ALWAYS turn into fanwank.

I'm somewhat more lenient if something was clearly set up as a narrative mystery to begin with (e.g. who is future guy? What did the Jurati-Borg try to stop?). But EVEN THEN - these stories are discontinued, and any "explanation" would inevitably be either fanwank or not really fit with the original story.

So, in my opinion, only go back to these "open questions" if it fits really, really well into a story that the writer wants to tell. The new story must come first. If it fits, fine. If not, don't reference it. Don't bend over backwards to find a solution for a question no one really asked for (e.g. "why do Klingons in TOS don't have ridges?")
 
Don't bend over backwards to find a solution for a question no one really asked for (e.g. "why do Klingons in TOS don't have ridges?")
I don't know what the plan was for Enterprise before it got cancelled, but I got the impression that they were going to start using the TOS Klingons in later seasons, so they needed to be reintroduced first.
 
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