Hold factions, motives, and methods constant. Put results in doubt.
Forgive the age of my examples, I was really only involved in World of Warcraft in the early days. Some of this is also going to be, like, Warcraft 3 stuff? It should still be understandable, though.
I'll lead off with an example, considering Scholomance as a result. Specifically, it's the result of the Barov family, an ambitious organization that wants to secure an immortal legacy, negotiating a deal with the Cult of the Damned, an arcane enemy that wants to spread the scourge of undeath, who tempted the Barovs with promises.
The factions here are the Barov family and the Cult of the Damned. Their motives, the end goal of the factions, are to secure an immortal legacy and spread the scourge of undeath. While each faction has a variety of methods at its disposal, the ones that came into play to make Scholomance are the Cult of the Damned tempting someone with promises and the Barovs negotiating a deal with them.
You can see, I hope, how a sufficiently motivated investigative squad that doesn't play by the rules but dangit they get results (you know, some player characters) could break up the result of Scholomance without necessarily having to annihilate the Barov family or the Cult of the Damned - they disrupt the negotiation and expose the cult's promises to the larger Alliance.
But, because the Barovs and the Cult of the Damned aren't annihilated, they can still try to progress toward their motives by other methods. The Barovs might decide to secure their legacy by forming a Merchant's Alliance and starting a civil war, absorbing other important merchant factions and claiming territory or resources. The Cult of the Damned could operate around the edges of the war looking for a way in, spying on the Alliance with scrying spells and recruiting followers or toadies. By creating factions with a motive and a variety of available methods, you can let the PCs act and succeed as they've earned and react to what they've done, rather than facing a sudden unexpected twist and making a rash decision when you're flat-footed.
Factions Are
As an introduction, let me break something to you: you are going to overshadow your players. It's an unfortunate maths consequence, at least if you're playing something in the conventional model of RPGs, where your players get one character each and you're left with the entire rest of the world. Your players won't be able to so much as pay a coin for an ale without you signing off on the people who grew the grain, drew the water, ran the brewery, carted the product, dug the gold, minted the coin, and made a society that accepted those coins and kept its roads secure.
Now, I've never heard of anyone getting rage-quittingly fed up over having to pay someone else's coin for someone else's ale in someone else's country; it's likely because nobody in that process actually wishes the PCs any particular ill will. Put a pin in that for later.
A faction is, well, all those people. It's especially important when adapting a Blizzard property to remember that a faction is all those people, when you're staring down the barrel of hero units and raid bosses and mission-critical NPCs. The Alliance is more than King Wrynn. If King Wrynn goes out for diplomatic talks and catches an unfortunate case of mace to the face, there are stormy times ahead for the Alliance but it's not going to just disintegrate. It's not made up of otherwise disinterested people subject to King Wrynn's single unifying will, but rather of people who see something worthwhile in keeping it going, even if it's nothing grander than doing right by the people they grew up with. Put a pin in that for later, too.
Even with those factions where there is more of a single unifying will, like the Lich King, there are still other distinct personalities, both within his thralls and outside them in allied groups like the Cult of the Damned, who aren't acting in blind accord with him but have their own ideas how best to accomplish the faction's motives.
When I'm talking motives I'm talking big goals, long-term goals that will change the faction or even the world forever if they're accomplished. Everyone who shares those motives is part of the faction. There are many ways those motives could be realized; when deciding on shorter-term actions for a faction to take, that's where its methods come into play.
Method Acting: or, The Threatdown
Those readers familiar with Powered by the Apocalypse (PbtA) have probably realized by now that I'm shamelessly renaming the concept of "threats" in those games, and related terminology. Ways to organize how all the people with desires out there will act to make and take trouble for and from the player characters. An important part of defining the genre for those games is to define what the broad categories of threats are and how they tend to act - their "moves", or, in my parlance, their methods.
In this case, since you're dealing with largely a fantasy setting, to create that headline example of Scholomance I pulled a couple of faction types from Dungeon World, a fantasy-genre PbtA game. You can see the complete list of types on the github here; each type has a half-dozen different moves associated with it, but for our purposes here you don't need to think of them as anything more than plot inspiration, ways to plan out the more immediate circumstances that you'll actually present the PCs with, to overcome according to the rules of your game.
When you're coming up with a "result" for the PCs to contest, use the faction methods for inspiration, but also consider how you can put it in doubt - the individual actors involved, the progress as it's visible to the PCs, and how the PCs can put a stop to it without necessarily annihilating everyone involved.
Pulling Pins: or, Slants and Scopes
When you start thinking about your campaign as a bunch of impending results of actions from factions, it's important to also remember those two pins from earlier.
People have their own reasons for remaining in the Alliance, rather than just blind accord with King Wrynn's single unifying will. Well, that's not unique to the Alliance, it's true of all the factions, so it's important to consider PC-NPC relationships. Within a faction there are people who all share common motives but who don't need to agree on or with the faction's current methods or desired short-term results. While there's certainly some fodder there for thinking about how the PCs are going to deal with the more overtly hostile factions they'll confront on their adventures, it's also useful for dealing with the factions the PCs are allied with or work for - what Apocalypse World would call the home front.
Suppose that the PCs support their allied faction's motives, but wind up at odds with the faction leadership, either because of their personal goals or difficult compromises they had to make. That doesn't mean that everyone in the faction is going to act as a monolith and shun them. Odds are there are probably some people who agree with the PCs and support what they've done. Let them surface, to find and support the PCs, even if faction leadership would disapprove. Contrariwise, if the PCs generally agree with faction leadership and act accordingly, odds are there are probably some people who disagree with the PCs and oppose what they're doing. Not to the point of, like, weapons drawn or poison in the ale, necessarily, but if you let them surface they can add some drama to a return to allied territory, making it a little spicier than just going shopping and headbutting everyone with an exclamation point over their heads.
Nobody ever complains about having to buy an ale with a coin in a society because none of the backers to that transaction wish them ill. Well, imagine what would happen if someone did, and knew they could take an action that could travel down that chain and hit the PCs. How do the PCs experience that? If it's anybody but, like, the tavernkeeper, the threat starts in a place and time so far remote from them that when it hits all they can do is frantically dodge and flail around in confusion. Who did that? What do we do now? This touches on matters of PC agency, and it's why Apocalypse World suggests starting with threats near to the place the PCs are, contesting the things they already care about, who they at least have some idea of how to deal with. While the PCs are acting, time moves on and things happen all over the world of Warcraft, but you don't need to make all of them into the whole faction/method/motive/doubt/result treatment. If they're not going to collide with anything the PCs care about, just advance that timeline like nothing happened.
Contrariwise, if something is going to collide with something the PCs care about, the PCs should have some way to know about it, however remotely it might start. I mean, it's great drama when some mysterious force drops from the heavens and overturns the world in an instant, but what's that like to live through? Everything you cared about, your life's work, gone in an instant, and you're helpless. What was the point of it all? Is there a point in going on? Your players are there not just to enjoy the drama of your world but also to enjoy living in it, and while there's some give and take, don't annihilate one for the benefit of the other. Say that an astronomer or astrologer or prophetic dream or whatever portends that something is moving in the heavens, and in three weeks it will fall on Stormwind with tremendous force. Even if the PCs aren't intended to stop it, they at least have a chance to save some of the things they care about, their life's work, and the things they do can have a point. And who knows? They might surprise you.
