While I don't need this show to be self-serious or morally ambiguous, the writers can't raise this very issue without exploring how the characters feel about what they've done. We know they were guilty of the crimes they were charged with because we've seen them commit the crimes.
The real problem is that it's way too late to suddenly be raising this issue. The show has shown very little interest in the logic of WHY these people are in Pegasus to begin with. Is it a) because Earth is desperate for Ancients tech with which to defend itself (in which case, how does the end of the Ori threat impact that desperation?) or b) because SGC has unilaterally decided to be intergalactic do-gooders, regardless of the mess they make in Pegasus or the threat this activity inevitably brings to Earth (in which case, how do they rationalize not allowing the people of Earth to know what's going on?)
With such fundamental questions unanswered, the whole trial situation makes no sense from a story standpoint.
Are their activities "crimes"? By whose standard? What motivated these "crimes" in the first place? Most of their crimes are actually just blunders. Were they blunders that had to happen, because something big was at stake? If nothing important was at stake, even then, they aren't crimes so much as really, really stupid and aggravating blunders.
The audience has no real way of judging the Atlanteans' behavior, other than I suppose being expected to have a mindless loyalty to Shep et al because they are Our Heroes and the other guys are nobodys we'll never see again and aren't very cool anyway. It's all too contrived and the outcome of the story is as rigged as the trial was, so why should we even bother to think about this? (I'm only doing it because it's fun to remind myself how truly bad this show really is.

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But they are guilty, aren't they? To a certain extend. At some point the Wraith and Replicators are responsible for their own actions of course. But causing these things to happen does require Earthlings.
They're guilty of making mistakes. Whether this is forgivable from the audiences' standpoint depends on something we don't know: are they in Pegasus for a or b as outlined above?
If it's a, then the judges won't consider that extenuating circumstances, because they don't give a flip about Earth's safety. But the audience is from Earth, so we'll consider their actions justified and we don't give flip about Pegasus' safety, certainly not enough to risk ours.
If it's b, then the whole Atlantis mission is sheer idiocy and neither Pegasus nor Earth should be expected to appreciate being placed in danger by nitwits. Even then the only crime is criminally bad writing.
I've been through this enough times, but no they aren't. Sheppard and co woke up ONE Hive. In return they have destroyed several. Sheppard sold his team short, they have done a lot of damage to both the Wraith and the Replicators.
That logic only works if they've been deputized by the people of Pegasus to act in their behalf, to make the decision that it's ok to get a thousand Pegasans killed in order to save a million. Trouble is, when exactly was this vote taken?
That's the problem in acting on behalf of outsiders who haven't made their wishes fully known (or even if they have; who's to stop them from changing their minds midstream when the going gets tough?) Maybe they'd prefer to take a chance a million of them would be killed tomorrow rather than the thousand killed today. Who is Atlantis to make that decision for them? Maybe it's a dumbshit decision but it's their dumbshit decision to make.
The ONLY way Atlantis are justified is if there is an overriding need for Ancients tech in order to defend Earth from a threat that can be fought no other way. This connection has never been made, it's hardly even been implied. And even if that's the rationale, exactly what threat is Earth facing right now? I thought Cam Mitchell conquered all.
