Bring a large pot of salted water to a boil and cook penne pasta until al dente. Reserve 1/2 cup of pasta water, then drain.
In a large skillet over medium heat, cook chopped bacon until crisp. Remove bacon with a slotted spoon and set aside, reserving the rendered fat in the pan.
Add diced chicken to the skillet and cook in the bacon fat over medium-high heat until browned and the internal temperature reaches 165°F (74°C). Remove chicken and set aside.
Add the butternut squash cubes to the same skillet. Cook for 8-10 minutes, stirring occasionally, until tender and caramelized.
Add Brussels sprouts to the skillet with the squash. Sauté for an additional 7-8 minutes until the sprouts are tender and charred on the edges.
Stir in the minced garlic and dried thyme, cooking for 60 seconds until fragrant.
Add the cooked pasta, chicken, and bacon back into the skillet.
Drizzle with olive oil and sprinkle with Parmesan cheese. Toss thoroughly, adding reserved pasta water 1 tablespoon at a time if needed to emulsify the sauce.
Season with salt and black pepper to taste before serving.