Preheat oven to 400 degrees F and line a baking sheet with parchment paper.
Cut the spaghetti squash in half and remove seeds. Brush insides with oil and sprinkle with salt and pepper to taste. Place the squash halves face up on a baking sheet.
Next, prepare the sauce. In a large skillet or pan with a lid over medium heat, warm the oil. Then, add the shallots and sauté for 2-3 minutes, or until translucent. Add the minced garlic, dried basil and sauté for another 30 seconds, stirring constantly to prevent burning.
Add the red lentils, water, and marinara sauce, and stir to combine. Bring to a simmer, then lower the heat, cover, and let the marinara sauce simmer for 30 minutes. Stir every once in a while to prevent the lentils from sticking to the bottom.
Divide the lentil marinara sauce between the squash halves, then bake on the top rack for 35 minutes.
After 35 minutes, top the squash with a thin layer of mozzarella cheese, then bake for an additional 20 minutes on the top rack, or until lightly browned and bubbly. (You can broil for 1-2 minutes if needed, but the cheese browns VERY fast under the broiler!).
Let cool for 5-10 minutes, then top with fresh basil and red pepper flakes and enjoy!
Storage: Store leftovers in the refrigerator for up to 3 days. Reheat in the microwave.
Notes
The nutrition facts are written as if 1 squash half was 1 serving.
You can omit the lentils from the marinara, but I like the added protein and nutrition.