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Spread the eggplant slices over the pizza pan to cover, overlapping the slices so that no pan shows through. Brush the eggplant generously with the remaining olive oil and sprinkle with salt and black pepper. Bake until the eggplant begins to brown, 10 to 15 minutes.
Spread the pizza sauce or pesto over the eggplant, and then top with the cheese, onions, olives, tomatoes and bell peppers. Sprinkle with red pepper flakes. Return to the oven and continue baking until the cheese is melted and begins to brown, about 15 minutes longer