Preheat your oven to 400°F and line two large baking sheets with parchment paper to prevent sticking.
Pour the milk into a shallow dish and in a separate dish, combine the breadcrumbs, 1 cup of Parmesan, oregano, thyme, red pepper flakes, salt, and several grinds of black pepper.
Dip each eggplant slice first into the milk and then press it firmly into the breadcrumb mixture, coating both sides evenly. Use one hand for wet dipping and the other for dry coating to keep it clean.
Arrange the breaded eggplant slices on the baking sheets in a single layer. Drizzle lightly with olive oil and bake for 18 minutes, flipping once, until golden and tender.
Spread 1/2 cup marinara sauce across the bottom of a 9x13-inch baking dish. Layer half of the baked eggplant slices over the sauce, then top with 1 cup marinara, half of the lentils, and half of the mozzarella slices.
Repeat the layering process with the remaining eggplant, marinara, lentils, and mozzarella. Sprinkle the top with the remaining 1/4 cup Parmesan cheese.
Bake the assembled dish for 20–25 minutes, until the cheese is melted and bubbly. For extra browning, broil for an additional 2–4 minutes on low.
Remove from the oven, top with fresh basil leaves, and serve warm. Enjoy!