Preheat your oven to 400°F and line two baking sheets with parchment paper. Set up your breading station with one shallow bowl for the beaten eggs and another for the panko mixture. Having everything ready before you start keeps the process moving quickly and mess-free.
In your second shallow dish, combine the panko, 1 cup of the grated Parmesan, oregano, thyme, red pepper flakes, salt, and a few grinds of pepper. Stir it well so the herbs and cheese are evenly distributed throughout the crumbs. This mixture is really where all the flavor and crunch come from.
Dip every eggplant round into the beaten egg first, letting the excess drip off. Then press it into the panko mixture, coating both sides thoroughly. I like to press down gently so the crumbs really stick and don't fall off during baking.
Arrange the breaded slices in a single layer across your two parchment-lined baking sheets. Drizzle generously with olive oil, then bake for 18 to 25 minutes until they're tender and deeply golden brown. The oil is essential here since it's what crisps up the panko without frying.
Spread about ½ cup of marinara across the bottom of your 9x13-inch baking dish. Add a layer of the baked eggplant slices, followed by another cup of marinara and half of the sliced mozzarella. This first layer sets the foundation for the whole dish.
Add the remaining eggplant, then the rest of the marinara and mozzarella. Finish with the last ¼ cup of Parmesan, a light drizzle of olive oil, and a pinch of sea salt. Seasoning between every layer keeps the flavor consistent from top to bottom.
Bake the assembled casserole for about 20 minutes, until the cheese is melted and bubbling. Then switch your oven to broil for 2 to 4 minutes, watching closely, until the top turns golden brown in spots. This final broil is what gives it that irresistible bubbly, browned cheese top.
Let the casserole sit for about 5 to 10 minutes before slicing so the layers can set. Scatter fresh basil leaves over the top right before serving. That resting time makes a real difference in how cleanly it slices.