Stack several pieces of Swiss chard on the work surface. Remove stems and set aside. Roughly cut leaves into pieces about 2-inch square. Repeat with the remaining swiss chard. Wash.
Heat oil in a large heavy skillet over medium high heat. Add chopped chard stems, garlic, onion, salt, thyme, nutmeg and pepper and cook, stirring often until the onions are starting to brown, 6 to 8 minutes.
Add chopped cleaned Swiss chard leaves, 2 tablespoons water and cover. Let wilt, 2 to 4 minutes. Remove lid and continue cooking, stirring occasionally until the Swiss chard is completely wilted and softened, 1 to 3 minutes.