Begin by cooking the pasta. Before draining, reserve 2 cups of the pasta water; then drain the pasta.
Meanwhile, brown the bacon in a large skillet over medium heat. Remove the bacon pieces to a paper towel-lined plate.
In the pan with the bacon fat, add the onions, garlic, and thyme. (If you feel there is too much bacon fat in the pan, remove some carefully with a paper towel.) Cover the pan and cook, stirring occasionally, until the onions just begin to brown (about 15 minutes). Then uncover and cook until gold brown for an additional 5-10 minutes.
Next, remove the pan from the heat. Add the cooked pasta to the onion mixture. Then add 1 cup of the reserved pasta water and the bacon. Crumble the goat cheese over top. Season to taste with salt and pepper. Toss until combined and the goat cheese is melted. Add more pasta water, if desired.