Heat a large skillet to medium-medium high heat. Once hot, spray with non-stick spray and add bacon. Cook for 3-4 minutes per side until bacon reaches desired crispiness. Set aside and crumble. Leave approximately 1-2 tbsp of bacon fat in the pan to cook chicken. Leave the heat on.
Now add the chicken pieces. Cook for approximately 5-7 minutes, continuing to toss so all sides are lightly browned. Set aside with bacon. Chicken may still be slightly undercooked, this is fine since they will cook more a bit later. Keep heat on.
Now coat the pan with 2 tbsp oil. Toss in onion, butternut squash, and brussels sprouts. Cook for another 5-7 minutes, until veggies become slightly browned and crispy. Now add in apples, chicken, and bacon. Toss around so all ingredients begin to flavor each other. Stir in the salt and balsamic vinegar. Let cook for another 2-3 minutes.
Remove from heat, mix in pecans and pomegranate arils. Toss in fresh thyme, and additional salt to taste. Serve hot!