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Turn on the oven to 400 degrees.
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Peel and slice the shallot thinly. Tear the sage leaves in small pieces and put both the sage leaves and shallots with heavy cream in a small pot over very low heat for fifteen minutes. Add the salt and the black pepper. Stir often and do not let the cream get to a boiling point.
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Meanwhile, slice off the neck of the butternut squash and trim off the stem end of the squash. Use a vegetable peeler to peel the skin off the squash. Peel the bottom half of the squash, slice in half and scoop out the stringy pulp and seeds out. Using a mandolin or a very sharp knife, slice the squash into very thin slices, about 1/8th of an inch thick.
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Taste the cream for seasoning and add more salt and pepper to taste if needed. Strain the cream and discard the solids.
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Butter a 9 x 13 inch casserole dish on the bottom and sides.
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Create one even layer of butternut squash in the dish, spoon on and spread a thin coating of the cream on the squash and repeat the process until the the last layer is topped with cream. Sprinkle the cheese on top of the cream evenly.
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Cover with aluminum foil and bake for 35 minutes. Remove the foil and turn up the heat to a high broil until the cheese is melted and golden brown (about five minutes, but watch carefully so it doesn't burn) and take out of the oven.
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Let the squash sit for 10 minutes and serve.