Preheat the oven to 350 degrees and spray a glass pie dish with cooking spray.
In a pan over medium heat saute the onion in the olive oil until tender, approximately 3-5 minutes. Add the chopped tomato and season with a pinch of the salt and pepper. Cook for another 1-2 minutes and remove from the heat.
Stir in 1/4 cup of the fresh basil, setting aside the rest for the topping.
While the vegetables are cooking, whisk together the eggs, milk, flour, baking soda and the rest of the salt and pepper.
Put the vegetable mixture in an even layer on the bottom of the pie pan. Sprinkle the cheese on top of that.
Carefully pour the egg mixture on top of the vegetables and cheese.
Carefully lay the tomato slices on the top of the eggs.
Bake for 35-40 minutes or until a tooth pick comes out clean.