Cook the bacon in a large skillet over medium heat, stirring occasionally, until crisp and brown, about 6 minutes. Use a slotted spoon to transfer the bacon to a paper towel-lined plate and pour off all but 2 tablespoons of fat from the pan. Return pan to heat and add squash and onions. Cook, stirring frequently, until squash is tender and onions are translucent, 7 to 10 minutes. Season with ¼ teaspoon salt and pepper. Allow mixture to cool slightly.
Place several pieces of foil in the bottom of a 6-quart slow cooker in an even layer. Set the pie crust onto the foil. (The crust should still be in its disposable tin.) Adjust as needed to allow pie shell to sit flat.
Spread the bacon and the squash and onion mixture into the pie shell in an even layer. In a medium bowl, whisk together the eggs, heavy cream, nutmeg, and ¾ teaspoon salt. Pour half of the mixture into the pie shell, covering the bacon and squash filling. Sprinkle the sage and half of the cheese over the egg mixture. Repeat with remaining egg mixture and cheese.
Cover the slow cooker and cook on low for 3½ hours until the filling is set and the crust is light golden brown and flaky. Serve immediately or keep warm until ready to serve.