There is a status defined as Good which Evil is trying to topple. The nature of the status quou depends on whether evil or good is control at any given point. Either the status is one of a largely just and fair society which is threatened by growing corruption from within, threats from without or a combination of the two. Or the status is of a terribly oppressive regime and the attempts to bring it to a final end.
In order to be interesting, Good and Evil would have to be relatively equal forces. You get this sometimes, with people talking about the "balance" between Good and Evil. Which is, as far as I'm concerned, ridiculous. This is especially the fact when you start realizing that in all of these stories where a balance between Good and Evil exists, that it is always Evil threatening the balance and that when things are balanced, that there's precious little of the Evil to be witnessed in the setting.
At this point someone will probably bring up the Kingpriest of Istar from Dragonlance, the Spanish Inquisition, witch hunts, or any other time in fiction or history when some nominally good religion was the source of much suffering and destruction. These are not examples of Good out of balance. These are examples of times when evil people believed themselves to be good.
Going to the original, basic meanings of the words "good" and "evil" basically come down to this: things are "good" when they are helpful, healthy and prospering; things are "evil" when they are harmful, unhealthy and suffering. If something is causing harm to a person or society at large, then it is, by definition "evil". It might be an overall minor "evil" such as high fructose corn syrup, or it might be a bigger one such as inflated medical costs.
Most evil is accidentally inflicted such as, for example, you cutting someone off in traffic without realizing it, causing them to correct and miss the changing light, getting stuck there for a minute or so and causing them through a chain of other events to be late for work. You caused harm there, even if you didn't know it. It is probably a minor harm, or it could be a major harm. For example if the person in question has a history of being late and this was his last chance. It could even be a major harm that neither of you ever realize, such as if being late by two or three minutes prevents the other person from meeting a person with whom they could have had a wonderful conversation and eventually become significant others.
Some evil is inflicted deliberately, such as when you are in a fight and intend to hurt your opponent. Or when you are acting in defense to kill your opponent before they kill you or another person. More often it's when you make a cutting jab at someone who annoyed you, or complain to the manager of an employee who didn't do their job. Or maybe it is in telling a secret you know will cause someone problem.
Sin is something else again entirely. This is where you get to capital E, Evil. Sin is when you commit an evil act where the evil is the goal and purpose of the action. For example, one person enlists in the army and goes to war to defend their country, another joins the army for the pay and to support his or her family. In both cases the violence they do is evil, in the terms that it is causing harm, but not Evil since they're not seeking to cause harm for its own sake. A third person joins the army because someone he or she cares about was killed by X "enemy" and they want revenge. A fourth person joins the army and goes to war because it means he'll be allowed to kill people legally. Both the third and fourth person are sinning, one for seeking revenge and the other who just wants to be able to kill for no other reason than because he wants to.
Evil, being inherently unhealthy, is inherently self limiting. Good, being inherently beneficial, is inherently self-building. Upon realizing this, it becomes clear that Good will come out on top in the end, because Evil tends to weed itself out.
Another note is that sin and thus Evil actively requires choice and intention. Capital G, Good requires choice and intention, but normal everyday good just keeps trudging along regardless. As does normal everyday evil, really.
To which the likely retort would be the idea of all humanity getting destroyed by X intelligent entity being a situation where "Evil" wins completely. Ummm, no. On a universal scale, whether there is a God or not, humanity is largely irrelevant to such a concept of Good. All that would mean is that we're gone and possibly there's a person going around doing evil things such as wiping out whole planets. Though, planets are, largely, irrelevant on a universal scale anyway. It would be bad for us to die. It would be good for us to live. But whether we live or not is not important to a universal health. Even if every intelligent species were to die because some person did something ill-advised, that's not a victory for Evil since all choice and thus all "Evil" is now gone, but Good trudges along. Again, we are largely unimportant on a cosmic scale.
This cosmic unimportance and the fact that Good vs Evil is such a forgone conclusion is why that theme is not, in and of itself, as much of an interest to me. Which is not to say I don't like stories where it is a theme, but the fact is those stories aren't so much about a Cosmic scale as they are a smaller scale issue.
In Lord of the Rings, the macro-conflict wasn't Good vs Evil; it was the Free Peoples vs Sauron. Even in the Silmarillion, the highest point of cosmic conflict was Morgoth vs the Valar. Yes, I'm aware he was trying to pollute Eru's works, but consider that Morgoth didn't really stand even a breath of a chance against Eru, so that's hardly a conflict.
No, we aren't really interested in discovering if Eru can defeat the evil Morgoth in the story. That's a forgone conclusion. We aren't even really interested in seeing the results of the Valar and Morgoth directly fighting (at least more than once), since Morgoth and his followers are explicitly weakening as they grow older. We are instead interested in seeing if the Valar can save the elves before Morgoth kills or corrupts them all, or if the elves can maintain their righteousness while battling Morgoth or seeking the Silmarils.
The Battle of Good and Evil is interesting as a micro-conflict, as in within the heart of a particular person. This might be the heart of the entire story, but it is still a micro-conflict since it involves primarily only a single person.
In the Lord of the Rings, the battle for Good and Evil wages primarily within the hearts of Sam, Frodo and Smeagol with Sam outright rejecting Evil and persevering, Frodo eventually giving into despair and Smeagol almost outright reveling in his downfall. The entire last sixth book of the story hinges on the fact that Sam doesn't quit even when Frodo can barely think straight and Smeagol doesn't quit even when his desire is ultimately self-destructive.
Now, excusing the ridiculousness of Good and Evil portrayed as great cosmic forces that must be kept in balance, we'll go on to other such concepts. In Moorcock's stories, Law and Chaos are the cosmic forces that are always trying to usurp each other and dominate reality. In other stories it is Light and Dark or Life and Death, or some other such set of opposites.
While these cosmic collisions are more believable as forces that must be kept in balance and which can be equal in force and power, they are still not so interesting for me. The reason is because I like characters who have their own agency. Characters who are operating under the agency of "something else" are largely not as compelling.
But Luke, don't you play a lot clerics or religious types in your games? Aren't you rather a believer in some greater sky wizard guy who supposedly made the universe? To the first question, yes I do. To the second question, which is cribbed from some of the more virulently aggressive atheists I've encountered, not exactly, but yes.
Neither of those really represents a loss of Agency to me. Faith, from my perspective, is an active choice and thus one thing that to me represents my Agency because I am actively believing in something for which I have no scientific proof. It is my choice to believe and even then, I don't believe in this ridiculous idea of some invisible long-bearded wizard who will solve all my problems for me because I prayed hard enough (doesn't stop me from praying really hard for some rather selfish things, I'll admit). I have a body, a mind and Free Will, if God planned on solving all my problems, then why do I have these three things?
As to the other, yes, my characters very frequently are devout followers of some religion whether they're actually of X game's cleric class or not. However, to me, the cleric/diety relationship in most fantasy worlds and games is really more like an employee/employer relationship than it is a worshiper/deity relationship. Granted, a large part of that is me dismissing these other entities as the Creator and simply accepting them as some level of existence between a human and the Allmighty. In the same way I can accept working for a company in exchange for cash, I can accept a cleric following a deity in exchange for power, especially if both the cleric and deity have similar ideals.
The agency of my clerics has not been supplanted.
Once you start having characters as the agent/tool of X cosmic force, their agency is removed. They're not the one doing stuff anymore. It's not Bill I'm reading about, it's Chaos. And that's really...not interesting if that's all it's going to be.
Going back to the Belgariad, Eddings handles this well. Belgarion never really loses his Agency, the Prophecies nudge things along on either side, but neither really takes him over. The success and failure of his quest is all about his choice to attempt it and, even more so, his choice in HOW he performs the quest.
Stephen King also handles this quite well. While I haven't read his opus series yet, I have read numerous stories in which God or Gan takes a role in things through some person. In all the instances I have so far seen, the moment in which God acts through a person only occurs through the choice of a character to allow it. They are hounded throughout much of these books about making a choice, and often given to know what would happen if they fail to make a choice, but they are never overridden until they allow it and usually the moment when God acts through them is very brief.
By comparison, some guy who comes down as the avatar of a cosmic force is unappealing.
For my own stories, macro-conflicts are largely cultural, ideological or political. In Divine Blood, the conflict between Yomi and Nirvana are due to centuries of bad blood between them, starting with the Demons (or what they were before being Demons) attacking the Gods (or what the Gods were when they were still mortal). The conflict between the Immortals in power and the rogue Gods and Demons is largely over reincarnation: most consider it a mental health necessity, others consider it a spiritual suicide. Nominal allies Australia and the NAA are in conflict over the progressive replacement of fossil fuels with nuclear power.
In Bystander, the Faction Wars (as yet only slightly referred to), are occurring because of the Intelligence community in North America having differing views on what the right way to go is for dealing with new technology, peaks, new political developments and practically everything else. For most of the first few books of Bystander, both the good and bad guys will have at least some evidence to show that they are acting in the name of either the US Government, the North American Military Alliance, or both. America is very quietly in a state of multi-front civil war that even most of the government is not aware of. And most of the factions think they're doing what's best for the country/region.
See, Good and Evil doesn't really work on a macro-scale because an organization can't really be Good or Evil. Some might have a tendency toward one direction or another because of the kinds of people they recruit, but they aren't going to be a force for Evil or Good. An organization does not have a single operational will. It is a conglomeration of a multitude of individual wills who usually agree to aim for achieving more or less the same goals using more or less the same methods.
Macro-scale conflicts, such as between countries and organizations, are going to be multi-faceted on the face, but at the core it's usually going to be about resources with one group doing its best to deny the other group the resources they either need or feel they deserve. Whether this is rebels in an oppressive empire or terrorists in a peaceful republic, the dynamic pretty much remains the same.