Depending On How You Look At It...

'There is nothing either good or bad, but thinking makes it so'
--Hamlet, Act II, Scene II 

'The sinking of the Titanic must have been a miracle for the lobsters in the kitchen'
--Reddit user ElBretto

When I was an undergrad, I had a professor who was fond of pointing out that there's no free lunch in ecology. A tasty meal for a lynx means the end of a hare.

This same principle can be applied to thinking about plot outcomes. While the triumph of an individual hero and the punishment of an individual villain can be generally viewed a positive outcome, the 'good'/'bad' dichotomy gets a bit messier if you expand the conflict. This is even more true if the two sides are morally ambiguous, and victory for one does not represent a sweeping win for the forces of good.

It bothers me intensely that many stories-- with high fantasy being a particularly bad offender-- act as though the triumph of the protagonist means a guaranteed happily-ever-after wrap-up for all the characters in the world of the story. When you have a story with a reasonably small scale, such as a conflict between just a few individuals, a clear 'happily-ever-after' or 'tragically-ever-after' ending might be feasible. In these instances, the 'world' of the story is compressed to encompass just the focal characters.

In narratives set on a national scale (following a ragtag band of rebels as they take on the Dark Lord), it's harder to ignore the other perspectives on the story's outcome. First and most obviously, there are the bad guy's minions who got slaughtered in the course of the battles between good and evil. How do their families feel about that? That's assuming the minions actually volunteered their services and weren't just innocent victims of the Evil Usurper. Second, there's the ones who got away, as well as all the passive supporters of the Dark Lord. These people are not necessarily cackling Evil Overlord wannabes, and may have thrown in their lot with the Dark Lord for entirely prosaic reasons. But they're probably pretty displeased with how things turned out, especially if the new 'Good Guys' government is going to hunt them down and punish them.

Finally, there's the 'collateral damage'. Bluntly, all the neutral characters who got caught in the crossfire. These are the people whose cornfields got trampled in the Final Battle, the people whose sheep got stolen for army rations, whose houses got taken over and used as barracks, who got conscripted, who got buried in rubble when their city was indiscriminately shelled by drones. No matter what side they might have been sympathetic to, or if they even cared about the conflict beyond praying that people would stop sowing land mines in their orchards, they're not going to be instantly happy when the heroes emerge triumphant. And that assumes that when the Good Guys win, they are going to send in emergency rations and a team of mine-sweeping rats to help clean up.

If you want to go for an clean 'happy' ending in a story like this, I would recommend the following. First, don't sweep the 'collateral damage' characters under the rug. Address the challenges they'll be facing, and how the good guys plan to help them. Second, and just as importantly, show that the struggle was worth it. This means establishing both the problems of the starting status quo--make the Evil Overlord actually evil-- and establishing how much better the good guys are (not just because they've got the right genes!) in a very concrete way.