Heat a heavy bottomed pot over medium high heat and add sliced onions.
Cook until softened about 20 minutes.
Cover the pot but leave slightly ajar. Cook in the oven at 350 degrees F until beginning to brown, about 40-50 minutes. Check periodically so the onions do not dry out completely.
Next, place back on the stove and cook until the onions caramelize and begin to break down. This will vary depending on your onions. When the mixture begins to stick deglaze the pan with the white wine.
Cook for a few minutes to pick up the brown bits from the bottom of the pan. This will give it the rich flavor and color you are looking for.
Add the water, shoyu, balsamic vinegar, thyme, garlic, and black pepper.
Heat this to a simmer and then cook for about 10-15 minutes.
Taste for salt and adjust to your liking.
Serve with a rustic bread with a vegan cheese slice broiled and bubbly. I used a whole wheat bread from the farmer's market with a slice of Follow Your Heart Pepper Jack cheese.