Preheat the oven to 375°F.
In an ovenproof skillet over medium heat, heat the olive oil.
Sauté the onion and garlic until the onion is slightly translucent, about 5 minutes.
Add the squash and tomatoes, and cook for about 10 minutes, or until any liquid in the pan starts to evaporate.
Season with the paprika, red pepper flakes, salt, and pepper, and then create 6 wells in the mixture. Crack 1 egg into each well, and transfer to the oven to bake until the whites have set, 7 to 10 minutes.
Garnish with the basil, and serve.