Preheat the oven to 400°F. Set out a large rimmed baking sheet, a 9 x 13 inch baking dish, and a large skillet. Grease the baking dish and set aside.
Place the chopped butternut squash onto the rimmed baking sheet. Drizzle with olive oil. Then salt and pepper liberally. (This is the only time salt is added to the recipe due to the use of bacon, saltine crackers, and Parmesan cheese, so be generous.)
Spread the cubed butternut squash out into a single layer. Roast in the oven for 30+ minutes until the squash is soft and toasted around the edges.
Meanwhile, place the skillet over medium heat. Brown the chopped bacon in the skillet. Once crispy, add in the onions and garlic. Sauté for 3 to 5 minutes to soften the onions. Then stir in the chopped pecans, sage, and thyme. Sauté another 1 to 2 minutes, then turn off the heat.
Crush the sleeve of saltine crackers with your hands. In a small mixing bowl whisk the half-and-half and eggs together.
Once the butternut squash comes out of the oven, move it to the greased baking dish. Add in the bacon and onion mixture, and the crushed crackers. Toss well to mix, then spread out and an even layer.
Pour the egg mixture evenly over the casserole. Sprinkle the Parmesan cheese evenly over the top.
Bake for 20 to 25 minutes until the top is crispy. Serve warm.
Look for pre-chopped butternut squash in the produce department to save time. Fresh is best, but you can also use frozen squash.