Step 1Heat the oven to 350 degrees. Warm the olive oil and onion in a medium saucepan over medium-low heat. When the onion starts to soften, after about 2 minutes, add garlic and cook just until fragrant, about 1 minute more. Add three-fourths cup water, the wine, thyme, red pepper flakes and one-fourth teaspoon salt and bring to a low simmer. Cook 20 minutes.
Step 2While the liquid is simmering, combine the sliced tomatoes, olives, parsley and one-fourth teaspoon salt, or to taste, in a baking dish just large enough to hold the fish. Arrange the mixture in an even layer in the bottom of the dish.
Step 3Season the fish inside and out with one-half teaspoon salt. Bring the liquid to a rolling boil. Lay the fish on top of the tomato mixture and pour the boiling liquid over it all. The liquid should come barely halfway up the fish. Seal tightly with foil and place in the oven.
Step 4After 20 minutes, remove the foil and spoon some cooking juices over the fish. Replace the foil, seal tightly and return to the oven to cook until a knife easily penetrates the flesh and the top fillet begins to lift easily, about 15 to 25 minutes more, depending on size of fish.
Step 5Remove the fish from the oven and let it stand briefly before spooning more of the juices over the top and serving.