Preheat oven to 375 °F (190 °C). Lightly grease a 9×13-inch baking dish.

Brush both sides of eggplant slices with 1 tbsp olive oil and season with salt and pepper. Arrange in a single layer on a baking sheet and bake for 20 minutes, flipping halfway, until tender.

While eggplant bakes, heat remaining olive oil in a skillet over medium heat. Add onion and sauté until softened, about 5 minutes. Add garlic and cook 1 more minute. Stir in marinara sauce, oregano, basil, and red pepper flakes. Simmer for 5 minutes, then remove from heat.

In the prepared casserole dish, spread a thin layer of sauce. Layer half of the baked eggplant slices over the sauce, then spoon half of the remaining sauce on top. Sprinkle with half of the mozzarella and Parmesan.

Repeat layers with the remaining eggplant, sauce, and cheeses.

Bake uncovered for 25–30 minutes, until cheese is melted and bubbly and edges are golden.

Let rest for 5 minutes, then garnish with fresh basil before serving.