So, what happens to the bad guys (Black Hats in particular) -- those who don't get shot to death, blown up, fall off a parapet into a volcano, or good stuff like that, in particular?

Walking around administering coups de grace to the minions of the Evil Overlord is, technically, permissible under Agency guidelines, but usually frowned upon. It's one thing to tap folks who have been shooting at you (as you move past them), or who you are afraid might regain conscience and sound the alarm. It's another thing to take out the main bad guy, then retrace your steps and execute the wounded and unconscious. It irks the local authorities something awful, and it raises questions at the Agency as to your emotional stability and suitability for field work.

(Unless you're specifically ordered to leave no witnesses, of course.)

In some cases, you simply leave the remaining bad guys (minions, in particular) for local civil or military authorities to pick up. No sweat, beyond, if necessary, dropping a dime. Some might get away, but if the main mission goal has been taken care of, the incremental advantage of removing the remaining palookas from circulation has to be weighed against extra time in the field and the chance of something going wrong. Plus, the low-level mooks rarely have further info that's worth gathering.

If there is someone significant you've captured, the decision of what to do with him or her is usually defined in the mission briefing. If not, the field operative's judgment can come into play -- release them, bring them back for questioning, or turn them over (directly or indirectly) to the local authorities. Or, of course, take them out. If there's a security issue with letting them loose ("He's seen too much"), and they can be transported (especially if they have information that might be of value), the best course is usually to bring them back to the Agency (there are a variety of standard, secure ways to do this -- calling for pick-up, taking them to a safe house, etc.).

What happens to them, once the Agency has them? Well, presumably, they're interrogated. They might be turned, released, given over to the authorities, or simply eliminated. Certainly some of them have resurfaced later on. Others have not.

But that's need-to-know, and, generally speaking, you don't.

It's worth re-noting, in this context, that IX is extraterritorial and extragovernmental, and thus is not beholden to any particular national laws (or, for that matter, international ones). While there is a sensitivity to the letter and spirit of local laws in most "friendly" countries, that appears to be as much a matter of self-interest as anything else. IX follows its own code and laws.

Or, looked at another way, IX will make use of a particular nation's legal system to deal with criminals and the like that it apprehends if it matches the Agency's mission; in any case, it disposes of Black Hats (and Grey Hats) as it sees fit.

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License To Kill