Arrange eggplants spoke-fashion, stems toward the center, around the inside rim of a 2-quart souffle dish. Place tomatoes in center. Scatter fennel on top of eggplant. Tuck garlic, basil, and thyme between vegetables. Pour oil, water, salt, and pepper over all. Cover tightly with microwave plastic wrap. Cook in microwave oven at 100 percent for 15 minutes.
Remove from oven. Uncover and let stand for 3 minutes before serving.