Eggplant Parmigiana

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For the sauce: 

2 tablespoons extra-virgin olive oil

2 small onions, halved and thinly sliced

3 cloves garlic, grated 

Kosher salt

1 1/2 teaspoons red pepper flakes

1 1/2 teaspoons sugar

One 28-ounce can plus one 15-ounce can whole San Marzano plum tomatoes

For the eggplant:

1 medium eggplant (about 1 1/4 pounds), sliced into 1/2-inch-thick rounds

Kosher salt

1/4 cup all-purpose flour

Freshly ground pepper

3 large eggs

1 1/2 tablespoons whole milk

2 cups Italian-style breadcrumbs

1 1/2 teaspoons dried oregano

1 1/2 teaspoons fresh thyme leaves

Vegetable oil, for frying (1 1/2 to 2 cups)

12 ounces fresh mozzarella cheese, thinly sliced

1/4 cup grated Parmesan cheese (about 1 ounce)

2 cups grated provolone cheese (about 8 ounces)

Handful of fresh basil leaves, torn