An npc has information of whatever certain heroes, whom happen to be around the level of the villain requesting the quest is, trying to do something good... So we are told to talk to whom ever would pay for such thing to be stopped. Same on the other side... Notice it can be more than one villain needed and notice the way the npc appears could be by suddenly be walking in the way of a traveling villain or it could be through a note some police or good guy drops after the beating...
This simple concept makes it so full pvp flagged characters will always engage typically PVE scenarios as if a player character of the opposite side could be lurking in the shadows...
The place the-called-to-defend-the-boss-enemy appears could be by replacing the boss are aiding him depending on the amount of people in the party and the level of the enemies and equipment level... and he could decide to go a head and ambush the interlopers or wait for them at the end place where usually the most powerful npcs would be protecting him...
This can be also used on boring FETCH QUESTS by giving information of whatever fetch is being done and for various reason be paid to stop it...
IT could be interesting to have some quest where some slow cargo vehicle needs to be escorted... while the opposite faction would be ambushing... and also NPC could be deployed randomly in any part of the vehicles known path.
Gathering information quests could be the ones triggering this other quests... The more gathering information quests won by your side the more information on the opposite faction operations...
The other important thing is to be sure that the person failing a quest because of another character then it should be stopped from redoing in for 24hs this way they will not just quit and retake it wasting the time of the other players..
Also there could be a whole investigation quest which could be completed with many side quests, in different ways so in case the interlopers keep failing they still have a chance...
Another important thing about this type of quest is that the ambushes should be given vague information by npcs about where in the dungeon the interlopers are and whom might have then defeated...
These type of quests would be particularly good to be able to be designed by players... so the game would literally grow more and more complex in the alternatives to fail or partially fail...
It will also make it so sneaky players have something more dangerous and smart to sneak around... and detecting skills be actually possible and useful not just for open pvp.
If the quest designer or dungeon designer can be tied to actual existing plots this will create a chain of quests the devs will not have to deal with... Also the name of the authors should appear so the players could build a taste and choose to engage certain side quest just because the author creates the type of environment they are seeking... Because you know... Lovecraft was brilliant writer but it is not for all tastes... Though Douglas Adams Hitchhiker's Guide to the Galaxy is.