- Player Agency- this is a problem of all adventures with a pre-determined plot, but it is especially acute with a mystery focussed adventure. The DM wants to steer PC's towards a certain goal, but when the players want something else(as they often do) then he must step on the toes of Player Agency to do so. When the DM drags PCs where their players don't want them to go, they get frustrated/bored with the game.
- Player Skill- solving mysteries can be difficult, and additionally, what seems obvious to the DM may not be to the players. So what does the DM do when the party is stuck, besides throw a tasteless Deus Ex Machina at them?
Motivation to the Rescue
When I ran Polish Resistance, I dealt with the Agency problem by making the mystery totally optional. And it worked okay--some sessions the PCs focussed on solving the zombie problem, while others they spent running around the sandbox pursuing their own goals. Dave Sokolowski, in the "Keeping" Section of the "Masks Companion"(thanks TotGaD for the link), takes a different approach.
"My motivation? To stay away from tentacles."
Deciding the investigators’ introduction point is the most important decision relating to character generation the players will make—how do they know Jackson Elias? And how does his death suck them into the mysteries of the cult? While this is discussed elsewhere in this book, one point must be made here: the further your investigators get from their original relationship to Elias, the more difficult it will be to keep them engaged. All investigators need motivation, and Elias’ death is ultimately only one part of the puzzle.
The point is that players will be much more motivated to solve the mystery if their characters have a personal reason to. As DM you should take the time to connect each PC to the mystery and as the investigation progresses, more work will be needed to keep them connected. This doesn't force players to take the path you have laid for them, but in practice you will have less of a disconnect between the plans of the DM and the actions of the players. And a smaller gap means that it will be easier for the DM to improvise when the players do choose a path that he hasn't prepared for.
Examples from Shadows Over Bogenhafen
As an exercise, I'm going to brainstorm a few examples of how a DM could connect PCs to the mystery in Shadows Over Bogenhafen as per Dave's recommendation. I chose Shadows because I'm not the only player who has observed that it has this Agency Problem.
1. Murder of a Friend
Like "Masks", "Shadows" also pulls the PC's into the mystery with an NPC murder, that of an Dwarven drunkard that they meet at the festival. So I would attempt to connect the PC's more meaningfully to that Dwarf, so that they are more motivated to investigate/avenge his death. For our recent game that should be easy, given that 3 of 6 PCs were Dwarves. Upon meeting the Dwarven drunk, it would turn out that he was a well-known Dwarven hero, fallen on hard times, whose service to his race is a well known tale. Additionally, he was the personal friend of one of the PC's fathers and even saved his life once, etc.
2. Saving a Friend
One of our PC's was a noble, so in that case one could say that one of the lower-ranking cult members(all high-ranking personalities) is an old friend of his. The cult member confides in him that he's gotten in over his head and needs help. Then he disappears.
3. Getting Back What's Mine
Our party spent a long time getting the run-around from town officials, but never really encountered any harsher sanctions. Why not have them fine the party so that the party will want to prove their innocence. For instance:
The party has to check their weapons at the door upon entering the town hall. When they compain to a clerk, he offers to file a report for them that the official story about the Goblin was false. When they then go to collect their weapons, they are told that they are being fined 100GP for having filed a false report, and that their weapons are being kept as collateral against the payment of the fine. The PC's may pay the fine or not, but either way they now have a motivation to solve the mystery and thus prove their innocence!
4. Let's Rob a Cult
Our party was more interested in making some cash than bringing down a cult. So if I were to run this, I would slip some hints of riches to be gotten in bringing down the cult. For instance, in the message about the new temple being ready, I might mentions something about the Jewels for the altar having been delivered or something like that.