Place squash, chopped onion and one cup of water in a large lidded skillet. Cover and bring to a low simmer over medium/ high heat, cook until squash has softened. Drain well and set aside in a bowl.
In a medium bowl, mix together cracker crumbs and cheese. Add two pinches of nutmeg and stir half of the cracker mixture into the cooked squash and onions.
In another bowl, mix together the eggs and milk, then add to squash mixture.
Stir in 1/4 cup melted butter, and season with salt and pepper.
Spread into a 9x13 inch baking dish.
Sprinkle with remaining cracker mixture as well as the crumbled bacon. Dot with 2 tablespoons butter.
Bake in preheated oven for 25 minutes, or until lightly browned.
Remove and garnish with fresh parsley to serve.
Notes
Feel free to add your favorite seasonings to spice up the squash. Oregano is great.