How do you decide when or not it's important? Who gets to make that call? Under what authority? It obviously wouldn't be right for the villains to call the shots in that case as it would be an unfair advantage for them.
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I will note that the case of the Undersiders is under very specific circumstances:
1: Their crimes before Taylor defected were major, but they were (IMO, Partially) justified in the really bad shit's case, not intentional, or otherwise relatively minor by Villain standards.
2: They're really bad crimes declined as they did more acts like fighting the S Class threats and other genuinely altruistic stuff (Freeing Dinah, Taylor's acts towards her territory).
3: They were proven fighters.
4: They could probably be somewhat be relied upon to not go psycho without provocation.
None of these apply to say...the ABB or E88. That's my criteria.
I'm surprised it doesn't XD
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I'd generally see a genuine threat worthy of offering pardons to Volunteers as an active threat capable and willing of killing tens or hundreds of thousands of people who can be fought effectively by the Volunteers and whom is big enough of a threat that the volunteers are needed or an actual help.
So when exactly do you put your foot down? Where do the compromises stop and you draw the line?
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People like the ABB or E88 or the Teeth. Villains with large bodycounts of innocents who can't be relied upon to not go psychotic. Basically, the unreasonable ones who can't be bargained with and the true monsters. And when the threat stops of course, cause then the villains aren't necessary anymore.
So how do you define justice then?
When the major crimes I actually care about (I don't give a shit about a lot of minor crimes) stop, the people have made some genuine efforts to do good or are productive members of society, and they aren't monsters. Monsters need to be contained because they cannot be trusted and aren't rational.
For a real world example, say you have a guy who robbed a bank and assaulted a cop in the process of escape a year ago (And didn't kill anyone). Since then, he's stopped doing major crimes done something to contribute to society. Founded a company, got a degree and became a doctor or lawyer, or dedicated himself to public works. I don't see the necessity of punishing that guy, beyond possibly fining him for the proceeds of the bank robbery, since that's much more practical than doing the same to the Undersiders.
The scale of the crime isn't the same, but the scale of the redemption isn't either (Because Endbringers don't exist IRL).
Justice for me is complicated. For the most basic i'd put it, the end of the offending behavior and something to pay back for the crime.
No, but you do have the 'helpful' criminals for the most part not lifting a finger until it affects them directly. Leviathan attacking Singapore or something, heroes and authorities help for the good of all. Most criminals don't. Leviathan attacking Brockton Bay where they live? Only lifting a finger for your direct benefit, for good or ill, is barely commendable, certainly not enough for waiving due process and the consequences thereof. There is a reason why the Wormverse allows for villain 'flipping,' extralegal options such as Wards instead of Juvenile Detention, etc. There already is leeway for those on the wrong side of the law, but willing to turn over a new leaf.
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I was talking about the Undersiders after Taylor made her deal. The same Undersiders that went to the PRT the instant they recognized the threat from Edchina, and who traveled half way across the world to fight Behemoth in India. The standards i'm talking about don't apply to all criminals who fight S Class threats, just a small percentage of them.
Everything else aside, you're coming from an inherently flawed assumption. Because in the end, it wasn't brute force. It wasn't numbers. That's what Cauldron thought and they were wrong. It was organization. People working together. Information.
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I'm looking at it from an in universe moral perspective, and that means actually looking at it from the perspective of the people involved. Otherwise the best, the most moral choice is to munchkin the fuck out of a bunch of different powers using OOC knowledge to smash Zion and the Endbringers from surprise, then steamroll the remaining villains who don't surrender before your might.
Villains take advantage of the weak spots in society, prey on it, widen it to their benefit, actively sabotage attempts to fix it. Villains contribute to anarchy. Banding together in small groups, tribalism, "screw you, I got mine," eroding morale. All of which are detrimental to the end goal of survival. You don't want that continuing. There is a reason why "warlords" are third world countries, notoriously unstable and those at the bottom suffer.
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Except again i'm talking about the Undersiders after Edchina and Taylor's deal, who are all intents and purposes retired from active villainy and continued to fight the Endbringers.