"Every fairytale needs a good old fashioned villain." -Moriarty.
So, it sounds like their will be a lot of bad guys in Destiny. However we need something to make us hate the invading aliens, sure they destroyed most of humanity, but I get the impression that happened a little bit before the events of Destiny 1 take place.
What I'm saying is that we shouldn't be fighting a Hatfield and McCoy second generation war, our characters need a direct reason to stomp their faces in, and feel good afterwards.
Perhaps it will be something you discover, as you mop up a squad of Fallen, you're standing in a decades-old nursery, or maybe you'll discover bones of women and children in a bomb shelter. But if the game is going to have RPG elements it has to give proper incentive, otherwise the killing is just to enjoy the loot.
TLDR: Make us hate the aliens for more than just pushing us back, loot and the challenge of fighting is a good incentive, but we need to get a warm feeling by killing the enemy.
Any ideas on how Bungie should fuel the furnace of our Guardian's retribution?
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Hate is too obvious a direction. Better to align particular enemies with a certain ideal set that may conflict with the players. The whole "Bad guys are wiping out humanity, blah blah" tends to be done very poorly, often ending up in a black and white "They're so bad, we're so good" circle-jerk (Gears of War style). Hating an enemy we're supposed to kill isn't even necessary. I'll point out that in Shadow of the Colossus, the whole idea that we really had no reason to kill those creatures is part of what made it so compelling. Halfway through you begin to question what you're doing and the game is all the better for it. Similarly in Braid, you're never given any reasons why you're stomping on creatures and killing bosses. You just do it because that's what you do in platformers. [spoiler]The realization that you, as Tim, are the villain provides much of the magnitude in Braid's twist ending.[/spoiler] It's not as simple as making enemies we want to kill because they're bad. Sure they could do that, but that would be cheap and shallow. There are so many directions you can go with. The question is not really how to make enemies that are worth killing, but how to create conflict that is interesting and meaningful.