Pre-heat the oven to 400. Lightly coat a baking sheet with cooking spray and set aside.
In a large bowl, toss the eggplant cubes with one tablespoon of the olive oil and salt & pepper to taste until eggplant is lightly coated. Spread the eggplant in a single layer across the prepared baking sheet and roast in the oven for 30 minutes.
While the eggplant cooks, fill a pot with water, salt it, and bring it to a boil. Cook the spaghetti al dente according to package directions and drain, reserving about 1/3 cup of the pasta water.
While the water boils/spaghetti cooks, pour the remaining tablespoon of olive oil into a large skillet or sauté pan and bring to medium heat. Add the chopped onion and cook for a few minutes until onions are softened and almost translucent. Add the minced garlic and cook another 1-2 minutes until garlic is fragrant. Add the sausage and cook, breaking up with a wooden or plastic spoon, until meat is cooked through. Stir in marinara sauce and reduce heat to low.
When the eggplant is finished roasting, remove it from the oven and turn the oven temperature down to 375. Lightly mist a 7x11 baking dish with cooking spray and set aside.
When the spaghetti is finished and drained, add it to the sauce mixture and stir to coat. Add the roasted eggplant and the crushed red pepper and stir until combined. Remove from heat for about 10 minutes. Mixture will still be warm.
Add the mozzarella cheese, ½ cup of the Parmesan, and the 1/3 cup reserved pasta water to the pasta mixture and stir until well combined. Transfer the pasta mixture to the prepared baking dish and spread out evenly. Sprinkle the remaining ¼ cup Parmesan cheese and the bread crumbs over the top. Place the dish in the oven and bake for about 25 minutes or until the crumbs on top start to turn golden and the cheese in the pasta is bubbling throughout. Top with sliced basil leaves and serve.