I definitely agree with Umbran.
Derren's method might be fine enough for the party is in a room, and they fail to exercise due diligence, so they miss an opportunity.
But a big mystery, spread across many sessions, lots of clues starts crossing into a situation that is harder for the players to keep track of than the actual PCs.
I wouldn't even be sure the players are trying to solve it. All this stuff might be just background info and random encounters to them when all they came for was a dungeon crawl. Letting the BBEG win because of that will feel like a railroad to them because the GM failed to deliver the game type THEY came for and instead foisted this apocalypse on them.
I think Celebrim's on the right track. Stop the train. Inspect the engine. Make sure everybody's all aboard.
I think in any case, PC victory over the BBEG will be a bit weaker, once a solution is implemented. But you know what, winning your first T ball game isn't as good as hitting your first home run either. As Umbran says, they need to learn how to do this.
I think a minimal conversation needs to happpen first. Get some info on what the PCs goal is and why. This may advise you that they had no clue they were "supposed" to solve a murder mystery.
You need to find out why the players don't ask NPCs for info or help. They sound like they don't trust NPCs or don't realize they are a resource, or they want to be entirely self sufficient.
From there, either as GM or as an NPC "Detective", walk through the case with them. Have the NPC point out clues and connections, but let the PCs finish the work. The NPC, perhaps a retired detective, has been watching this case. He's not able to just "go solve it", but he wants to pass on his skills. So have HIM ask if the PCs have questioned so and so that a letter references if the conversation doesn't lead the PCs to think of that themselves.
An NPC like that to review the case and ask the questions of the PCs and info that they players aren't, may jog the Players onto what they need to be doing and how they need to be doing it.
Innerdude's idea of having a new mission from another NPC that just rams right into the BBEG or the mystery NPC is also a decent solution. It basically says, "the PCs will eventually run into the BBEG so we can finish this story". If the PCs are smart, they'll see the clues and get their sooner. if they are dumb, they'll bumble into it. Consider how many movies are just the latter... Afterwards, post-game discussion about all the symbols and clues will reveal that the answer was in front of them all along.
I don't see "pre-destined collision" as a problem or as a giveaway victory. In any single encounter, the PCs could die. So be it. Or they fail, and runaway. Unless the PCs die, that means they can try again, usually from a setback position (things are worse). Eventually they'll get there, or die. I don't have to escalate the bad guy's plan as a consequence of PC failure if the situation doesn't really warrant it. So the pacing can reasonably be controlled. And wiring up a final "this is so obvious you can't miss it" adventure to get the PCs to fight the BBEG (perhaps because he is now on top of the clock tower wiring up his doomsday machine with lightning going on all over and EVERYBODY knows something is up) is not a terrible thing.
If a few PCs get knocked off and fall to their death, so be it it. Destiny doesn't mean a few eggs won't get broken.
Derren's method might be fine enough for the party is in a room, and they fail to exercise due diligence, so they miss an opportunity.
But a big mystery, spread across many sessions, lots of clues starts crossing into a situation that is harder for the players to keep track of than the actual PCs.
I wouldn't even be sure the players are trying to solve it. All this stuff might be just background info and random encounters to them when all they came for was a dungeon crawl. Letting the BBEG win because of that will feel like a railroad to them because the GM failed to deliver the game type THEY came for and instead foisted this apocalypse on them.
I think Celebrim's on the right track. Stop the train. Inspect the engine. Make sure everybody's all aboard.
I think in any case, PC victory over the BBEG will be a bit weaker, once a solution is implemented. But you know what, winning your first T ball game isn't as good as hitting your first home run either. As Umbran says, they need to learn how to do this.
I think a minimal conversation needs to happpen first. Get some info on what the PCs goal is and why. This may advise you that they had no clue they were "supposed" to solve a murder mystery.
You need to find out why the players don't ask NPCs for info or help. They sound like they don't trust NPCs or don't realize they are a resource, or they want to be entirely self sufficient.
From there, either as GM or as an NPC "Detective", walk through the case with them. Have the NPC point out clues and connections, but let the PCs finish the work. The NPC, perhaps a retired detective, has been watching this case. He's not able to just "go solve it", but he wants to pass on his skills. So have HIM ask if the PCs have questioned so and so that a letter references if the conversation doesn't lead the PCs to think of that themselves.
An NPC like that to review the case and ask the questions of the PCs and info that they players aren't, may jog the Players onto what they need to be doing and how they need to be doing it.
Innerdude's idea of having a new mission from another NPC that just rams right into the BBEG or the mystery NPC is also a decent solution. It basically says, "the PCs will eventually run into the BBEG so we can finish this story". If the PCs are smart, they'll see the clues and get their sooner. if they are dumb, they'll bumble into it. Consider how many movies are just the latter... Afterwards, post-game discussion about all the symbols and clues will reveal that the answer was in front of them all along.
I don't see "pre-destined collision" as a problem or as a giveaway victory. In any single encounter, the PCs could die. So be it. Or they fail, and runaway. Unless the PCs die, that means they can try again, usually from a setback position (things are worse). Eventually they'll get there, or die. I don't have to escalate the bad guy's plan as a consequence of PC failure if the situation doesn't really warrant it. So the pacing can reasonably be controlled. And wiring up a final "this is so obvious you can't miss it" adventure to get the PCs to fight the BBEG (perhaps because he is now on top of the clock tower wiring up his doomsday machine with lightning going on all over and EVERYBODY knows something is up) is not a terrible thing.
If a few PCs get knocked off and fall to their death, so be it it. Destiny doesn't mean a few eggs won't get broken.