Heat the oil in a large skillet over medium-high heat. Add the thyme, garlic and onion and cook, stirring occasionally, until the garlic and onion are softened and golden, about 5 minutes. Stir in the tomatoes and bring to a simmer. Cook, stirring occasionally while breaking up the tomatoes, until the sauce is thickened slightly, 10 to 15 minutes. Season with 1 teaspoon salt and 1/2 teaspoon pepper.
Put 4 medium (8-ounce) ramekins on a rimmed baking sheet. Divide the sauce among them. Make 2 shallow wells in the sauce in each ramekin. Working with one egg at a time, crack the egg into a small bowl and then gently pour into one of the wells. Sprinkle the eggs with salt and pepper. Add the desired toppings to each ramekin. Bake on the baking sheet until the egg whites are set but the yolks are still runny, 15 to 20 minutes.
Serve with crusty bread for soaking up the sauce.
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