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 player-characters will:

* Have different priorities regarding what events to act on and what goals to pursue.
* Approach problems in a completely different way than 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 they trust or distrust.
* Have different opinions about what their moral values are, so they will 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 do their best to accommodate such surprises and diverge from the plot by improvising. A well-planned campaign should be able to cope with that divergence and still move forward even if the players don't always do what you expected from them. Remember that being a GM is not about telling *your* story. It's about developing a story together with the players.

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 progress? Does it still get resolved? (Not necessarily in the same way as you planned, but still in a meaningful way).