Heat olive oil in a large cast-iron skillet or heavy-bottomed pan over medium heat. Add diced onions and cook for 4-5 minutes until they become translucent and release their sweet aroma. Stir in minced garlic and red pepper flakes, cooking for another 30 seconds until fragrant.

Pour in the crushed tomatoes, followed by salt, pepper, oregano, and smoked paprika. Bring the mixture to a gentle simmer, then reduce heat to medium-low. Let it bubble away for 10-12 minutes, stirring occasionally, until the sauce thickens slightly and the flavors meld together. Taste and adjust seasoning.

Using a spoon, create small wells in the simmering sauce, spacing them evenly around the pan. Crack each egg into a small bowl first, then gently slide it into a well. The eggs should sit comfortably in the sauce without overcrowding.

Cover the skillet and cook for 8-10 minutes, depending on your preferred yolk consistency. For runny yolks, aim for 8 minutes; for firmer yolks, go the full 10. The egg whites should be completely set and opaque white, while the yolks remain golden and slightly jiggly. Remove from heat and let it rest for 2 minutes.

Serve immediately with warm crusty bread, garnished with fresh basil and grated Parmesan cheese.