Cod is low in calories and saturated fat. Marinating the fish in lemon juice intensifies the dish's flavor.
Preheat oven to 400 degrees. Place cod fillets in a nonreactive dish, and squeeze lemon on top. Refrigerate for 30 minutes. Sprinkle with 1/4 teaspoon salt, and season with pepper.
Heat 1 tablespoon oil in a medium Dutch oven over medium heat. Add onions; cook until golden brown, about 12 minutes. Add garlic; cook for 3 minutes. Remove from heat. Top with half the zucchini, tomatoes, and thyme. Drizzle with 1 1/2 teaspoons oil, sprinkle with 1/4 teaspoon salt, and season with pepper. Add cod and remaining zucchini, tomatoes, thyme, oil, and salt. Season with pepper.
Bake, covered, for 10 minutes. Baste with the juices, and bake, uncovered, for 15 minutes more.