The difference between writing a novel and planning an RPG campaign is that in a novel, you control the protagonists. In an RPG, the protagonists do what they feel like. That means not every plot which works well for a novel will also work well for an RPG. Especially when that plot hinges on the protagonists making certain decisions. When you are a GM in an RPG session, you have to be aware that the players will:
- Approach problems in a completely different way you imagined (use force when you expect puzzling, use puzzling when you expect diplomacy, use diplomacy when you expect force).
- Have a different opinion than you about which NPCs their characters like or dislike.
- Have different opinions about what the moral values of their characters are, thus make unexpected decisions when it comes to moral judgments.
- Won't share your estimation regarding what details in their surrounding are important clues and what details are just fluff.
A good GM will allow all that and a well-planned campaign should be able to cope with that divergence and still move forward even if the players don't do what you expected from them.
A test to see how well your plot works as an RPG is to imagine what happens when you replace the protagonist with someone with a completely opposite personality. Does it still get resolved? (Not necessarily in the same way as you planned, but still in a meaningful way)