Some great advice here, I'll just add a couple of things.
1) what seems obvious to the DM (and us reading this) is probably not very obvious at all to players. The players only really ever pick up on what you can help them understand, and often leaping to conclusions is difficult for most players. So keep your clues simple and obvious, and don't let a single failure become a road-block to progress.
2) a clue matrix is a good idea; personally I like a flow-chart or even just a simple kind of time-based list of what goes on whether the PC's do stuff or not. In this kind of adventure, the world doesn't stand still while the PC's try to figure it all out. Ideally, the longer the mystery remains unsolved, the more bad stuff happens until the PC's pretty much end up in the thick of it even if they are not ready.
3) try and set up the "what next", so it's the start of a campaign, not just a one-off adventure for level 1 adventurers. You only need some vague idea of a greater threat, or whatever, but there should be one or more loose threads that can lead into the next adventure.
As for pre-published material, as far as I know there is very little of this for D&D, which is a real shame. I ran a pretty good one for 3.5, part of the Living Greyhawk thing so I don't think it's publicly available. The key feature I liked was that there were a number of 'events' which happened at various times, that would intersect with what the PC's might be doing, and those gave them things to battle / investigate / etc, and also helped show how there was a lot of bad stuff going on caused by a particular NPC that the PC's had to hunt down and defeat before that section of the city was terrorised.
Personally I think your idea could easily be expanded into a level 1-3 adventure, where they fight the 'boss' monster(s) or whatever at level 3. After that, maybe it's found out that the monsters were just the prelude to something bigger and badder... You can make that part up later.
1) what seems obvious to the DM (and us reading this) is probably not very obvious at all to players. The players only really ever pick up on what you can help them understand, and often leaping to conclusions is difficult for most players. So keep your clues simple and obvious, and don't let a single failure become a road-block to progress.
2) a clue matrix is a good idea; personally I like a flow-chart or even just a simple kind of time-based list of what goes on whether the PC's do stuff or not. In this kind of adventure, the world doesn't stand still while the PC's try to figure it all out. Ideally, the longer the mystery remains unsolved, the more bad stuff happens until the PC's pretty much end up in the thick of it even if they are not ready.
3) try and set up the "what next", so it's the start of a campaign, not just a one-off adventure for level 1 adventurers. You only need some vague idea of a greater threat, or whatever, but there should be one or more loose threads that can lead into the next adventure.
As for pre-published material, as far as I know there is very little of this for D&D, which is a real shame. I ran a pretty good one for 3.5, part of the Living Greyhawk thing so I don't think it's publicly available. The key feature I liked was that there were a number of 'events' which happened at various times, that would intersect with what the PC's might be doing, and those gave them things to battle / investigate / etc, and also helped show how there was a lot of bad stuff going on caused by a particular NPC that the PC's had to hunt down and defeat before that section of the city was terrorised.
Personally I think your idea could easily be expanded into a level 1-3 adventure, where they fight the 'boss' monster(s) or whatever at level 3. After that, maybe it's found out that the monsters were just the prelude to something bigger and badder... You can make that part up later.
