Try Looking At It From My Side
As we steam along on story development for Son of Science Novel, occasionally our brainstorming sputters a bit. One reliable way to get the juices flowing again is to pick one of the secondary characters or villains and take a brief stroll in those shoes. It always shows us gaps that would otherwise be hidden, giving us fodder for discussion and interesting problems to solve.
Remember to make everyone in your story world a full citizen. The allies and enemies are not merely there as foils for the protagonist. They don’t vanish the moment the action moves away from their vicinity.
Try telling the tale in the villain’s voice. It will help make sure the bad guys’ actions are coherent and give your heroes worthier adversaries.