Preheat oven to 400 degrees F. Butter or spray with oil an 8x12 casserole dish and set aside.
Bring a large pot of salted water to a boil. Blanch the halved brussels sprouts for 3 to 5 minutes, until just barely tender. Remove from pot, drain, rinse with cold water and set aside.
Fry bacon until crispy, 8-10 minutes. Remove from pan and set aside on a paper towel-lined plate. Chop when cool to the touch.
Add the shallots to the bacon grease and sauté 4 to 5 minutes until softened. (If little grease remains, add a tablespoon of avocado or olive oil. You can also drain the bacon grease and sauté the shallots in oil instead.) Add the garlic and sauté 1 minute until fragrant. Stir in the flour and whisk for 1 to 2 minutes.
Add the milk and stir until well incorporated. Cook over medium low heat for several minutes, stirring, until the sauce thickens and coats the back of your spoon. Add salt, fresh thyme, and nutmeg.
Add cheddar jack cheese to the sauce and stir until melted and incorporated. Add half of the cooked bacon back to the sauce. Season to taste.
Stir the Brussels sprouts into the cheese sauce, and then transfer them to the casserole dish. Sprinkle with the remaining bacon and Parmesan cheese.
Bake for 20 to 25 minutes until browned and bubbling.
*Nutritional information is an estimate. Please consult a doctor or nutritionist for the most accurate nutritional info.