Antagonists do what they must
Everyone comes into conflict at some point, in real life and in fiction. We're all trying to do the best we can in a sometimes unclear environment, and that means that we aren't always going to see eye to eye. Sometimes things get out of hand, and the next thing you know, you're locking horns with a good friend. That doesn't make you bad; it makes you someone with a different view on the situation than your opposite number.
Pure antagonists are villainous in the right arcs, obstacles for other characters to overcome, but they're not becoming that way out of a desire to hurt anyone. At the time of this writing I'm in the middle of roleplaying a conflict between a Sith and her apprentice in Star Wars: The Old Republic, both of whom are fundamentally decent people but who are still irrevocably at odds. It doesn't make either one good or bad, but it does mean that by the end of an arc, one of them needs to lose out.
The key to making this work after the fact is one of two things. The first is the possibility of the antagonist coming to agree with the opposing side, either being shown the error of her ways or realizing what she's done. Rather than viewing her past actions as entirely justified, she must realize those choice were mistakes, a conflict she wishes to avoid in the future. It marks her as someone to be watched in the future but not someone with an overt agenda.
On the other hand, the antagonist could simply be circumvented. If she's trying to stop the Charr from killing something in Ascalon and the Charr manage to do so despire her best efforts, she's not going to be happy or be an ally again, but she's also lost just the same. There's no reason to knife her up (immediately) because she's lost and further conflict is meaningless. It gives a sense of resolution without having to inflict unwanted pain to the antagonist, and so long as there's no real crime, it's not as if you need to hunt her down. Heck, in a few months you might be on the same side of a debate.
Malice gets directed
Some people do not care about other people. There are human beings (and presumably elves or Vulcans or whatever) who have no problem compartmentalizing themselves into completely different groupings than others. In roleplaying, these are the characters who actively enjoy doing nasty things, chasing after power and control without any sense of shame or moderation. Webcomics in particular love having a character who has no shred of human decency to fall back upon and an endless amount of hatred for everything; you can name examples without even trying.
But here's the rub: These sorts of villains are genuinely good at something, which is inflicting pain without much direction. That's actually a worthwhile skillset at times.
A purely malicious villain, someone who has to be stopped because of the sheer suffering he inflicts, isn't necessarily targeting the characters. He's just targeting whoever is he can target without fear of recrimination. Under the right circumstances, these villains can be treated as a particularly angry animal. Point that malice toward a constructive end and it almost becomes an advantage.
Malicious characters are without scruples or much in the way of morality, and that means they're willing to do things that others might not be able to do without regret. Your fundamentally decent character can torture if she needs to, but she won't like it. A malicious bastard will gleefully torture his victim for information without a shred of remorse and move on without a care in the world. Sometimes the trick is just arranging the right problems for a hammer to treat as a nail.
Dealing with the devil
From there, we find ourselves dealing with villains that combine both aspects. Your character is an antagonist; she's in direct opposition to other characters. She's also downright awful. There's no reason for her to be left around, nothing that could be gained by not vivisecting her at the first opportunity...
Unless, of course, there is.
It's an extreme version of what makes jerks worth keeping around. Sure, the other characters would really like to kill Baron Von Puppymurder, but the Von Puppymurder family has a lot of connections, enough to ensure that outright killing the baron is a bad idea. You can stymie him, but every so often you might find out that you need access to the family fortune, and that means hoping that he's a forgiving man.
The villain doesn't even have to be a major power so long as he's got the right sort of power. There is an endless parade of criminals in most police dramas who are malicious little snots, but the cops let them off for the most part because they need to chase even bigger problems. Some villains are too useful to off.
Feedback is welcome in the comments down below or via mail to firstname.lastname@example.org, as in previous weeks. After three years, you're used to the routine. And speaking of three years, I think it's time for an anniversary column next week!
Every Friday, Eliot Lefebvre fills a column up with excellent advice on investing money, writing award-winning novels, and being elected to public office. Then he removes all of that, and you're left with Storyboard, which focuses on roleplaying in MMOs. It won't help you get elected, but it will help you pretend you did.