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Preheat the oven to 400 degrees F. Lightly coat an 8x12-inch or similar 2-quart glass or ceramic gratin or casserole dish with olive oil cooking spray. Set aside.
In a large frying pan, cook the bacon over medium-low heat until crisp, about 8 to 10 minutes. (Do not rush it or the bacon will burn before it is fully crispy.) Remove the bacon to a paper-towel-lined plate, pat dry, and let cool. Discard all but 1 tablespoon of the bacon drippings from the pan.
Place the pan back on the heat and increase the heat to medium high. Add brussels sprouts, onions, and 1/2 teaspoon kosher salt. Stir and cook until the onion is soft and golden and the brussels sprouts are crisp-tender, about 10 to 12 minutes. Add 1/2 cup water. Bring to a boil, then cook until the liquid is evaporated, about 2 to 3 minutes. Spoon the brussels sprouts and onions into the prepared baking dish. Carefully wipe the pan clean.
Melt the butter in the pan over medium. Once melted, sprinkle the flour over the top and whisk until the flour becomes golden, about 1 minute. Add the milk a few splashes at a time, whisking vigorously as you go to break up any lumps. Once all the milk is added, bring the mixture to a simmer. Continue to simmer, stirring often, until the mixture thickens into a sauce, about 2 to 4 additional minutes. Stir in the thyme, pepper, nutmeg, and remaining 1/4 teaspoon salt. Remove the pan from the heat and stir in the cheese until it melts. Taste and add additional salt or pepper as desired (remember that the bacon will also add some saltiness). Pour over the brussels sprouts, and with a spatula or the back of a spoon, spread the sauce evenly over the top.
Sprinkle the bread crumbs over the top of the brussels sprouts, then lightly coat the breadcrumbs with olive oil spray. Crumble the bacon, then sprinkle it over the top. Place in the oven and bake until hot and bubbly and the bread crumbs are golden, about 10 to 15 minutes. Serve hot.