Preheat oven to 400º. Place spaghetti squash on a plate and microwave 5 minutes. Halve each lengthwise and remove any seeds (be careful of hot steam!). Transfer to a parchment-lined baking sheet, season with salt and pepper, and drizzle with olive oil.
Bake, cut-side down, for 30 minutes. Remove from oven and heat broiler.
Meanwhile, in a small skillet over medium heat, crisp pepperoni, stirring occasionally. Transfer to a plate.
Loosen spaghetti strands using a fork. Add ½ cup marinara, ¼ cup mozzarella, and ¼ cup crispy pepperoni to each baked squash half. Mix filling with a fork and top with ¼ cup more mozzarella and parsley. Return to baking sheet.
Broil until cheese is melted and golden, 4 to 5 minutes. Serve immediately.
