You will need to peel the butternut squash, cut it in half - lengthwise and scoop out all of the seeds. Then it's a matter of cutting it into one inch cubes. A time-saver tip would be to buy already cubed squash from the produce section in the grocery store.
Once you have your squash cubed you can preheat your oven to 400 degrees and grease your 13" by 9" baking dish with one tablespoon of melted coconut oil.
Then core your apples and chop them up into one inch cubes. You can peel the apples if you prefer, though it's not necessary. I like to use a Honeycrisp apple but your favorite will work as well.
Place squash and apples in a large bowl. Rough chop your onion and then add it to the bowl. Add 2 tablespoons melted coconut oil, sage, and thyme to the squash mixture. Season with salt and black pepper, to taste, and toss to combine.
Transfer the butternut squash mixture into your prepared baking dish and spread into an even layer. Roast in the oven just until the butternut squash is fork tender, around 25-30 minutes.
While the apples and squash are roasting, prepare your topping by frying up the bacon. Heat a large skillet over medium heat and add the bacon. Cook, stirring occasionally, until the bacon is cooked through and crispy, approximately 8-10 minutes. Transfer the bacon to a plate lined with paper towels to absorb excess grease. Blot off remaining grease on top and set aside to cool for 5-10 minutes.
Once the bacon is cooled, crumble it into large pieces and place it in a small bowl. Add the remaining tablespoon of coconut oil, chopped pecans, honey, cinnamon, and ground cloves. Season with salt and black pepper, as desired, and toss to combine.
When the squash is done, remove from oven and top with the bacon-pecan mixture. Return to the oven until the topping is nicely browned, approximately 10 minutes. Remove from oven and cool for 5 minutes before serving.