Preheat oven to 425°F. Line a baking sheet with parchment paper.

Place the eggplant, olive oil, 1 teaspoon salt, and black pepper in the prepared sheet pan. Roast for 20 minutes, then flip halfway through, add the onions, garlic, crushed red pepper and return to the oven until the eggplant is golden brown and caramelized, 15 more minutes.

Meanwhile, bring a large pot of heavily salted water to a boil and cook pasta until barely al dente. Reserve 1 ½ cups pasta cooking water, then drain and rinse pasta under cold water.

Transfer the pasta to a 9x13 baking dish. Add marinara and stir as much reserved pasta cooking water as needed until the sauce is glossy.

When the eggplant is done cooking, transfer it on top of the pasta. Fold in the Parmesan cheese, 1 cup mozzarella and 1 cup basil. Top with remaining 2 cups mozzarella.

Lower the oven temperature to 375°F and bake until the sauce is bubbling on the sides and the cheese is melted, about 25 minutes. Top with more grated parmesan and torn fresh basil to serve.