Preheat your oven to 425°F (220°C) and let it heat for at least 10 minutes.

Wash and trim the Brussels sprouts, cutting them in half. Peel and cube the butternut squash. In a large bowl, toss the Brussels sprouts, butternut squash, sliced shallots, and chopped bacon with olive oil, kosher salt, and black pepper.

Spread the vegetable mixture in a single layer on a baking sheet and roast for 10 minutes. Toss gently, and roast for another 10 to 15 minutes until golden and tender.

Boil a large pot of salted water, add the pasta, and cook according to package directions until al dente (about 8-12 minutes). Reserve 1 cup of starchy pasta water, then drain the pasta.

In a skillet, heat 2 tablespoons of olive oil over medium heat. Add minced garlic and red pepper flakes; cook for about 30 seconds until fragrant.

Reduce heat to low and add the cooked pasta, roasted vegetables, crispy bacon, Parmesan cheese, fresh thyme, and lemon juice. Stir in reserved pasta water until a glossy sauce forms.

Taste and adjust seasoning with salt, pepper, or lemon juice as needed. Transfer to serving plates and garnish with more Parmesan and fresh thyme.