Preheat oven to 400° F. Line a baking sheet with parchment paper.
Gather 3 wide, shallow dishes (such as pie plates). In one dish, place the flour. In the second, whisk together the eggs and water. In the third, stir together the breadcrumbs, half of the Parmesan cheese and the pepper.
Coat the eggplant slices first in the flour and gently tap off any excess flour. Then dip in the egg, fully coating both sides of the eggplant slices. Finally, coat each piece of eggplant with the breadcrumb mixture and place in a single layer on the parchment-lined baking sheet.
Bake in the oven for 20 minutes, until golden brown. You do not need to flip the eggplant slices over during the bake time. Remove the pan from the oven and reduce the oven temperature to 375° F.
Spread about 1 cup of the marinara sauce over the bottom of a 13x9-inch baking dish. Lay half of the eggplant slices in a single layer over the bottom of the dish. Spoon half of the remaining marinara sauce over the eggplant, gently spreading it into a somewhat even layer. Sprinkle with half of the mozzarella and half of the remaining Parmesan cheese.
Repeat the layer once more, using the remaining eggplant, marinara, mozzarella and finally Parmesan on top.
Bake, uncovered, at 375° F for 25-28 minutes, until the casserole has browned on top. Serve with chopped fresh basil.