Preheat oven to 300 degrees F.
Season the deer roast all over with salt and pepper then rub with flour to coat.
In a large Dutch Oven, heat olive oil over medium-high heat. Sear the deer roast for about 3 minutes per side until browned.
Arrange sliced onions and minced garlic around the deer roast. Add apple cider, beef broth, tomato paste, thyme, rosemary, cloves, and cinnamon to the Dutch Oven and bring mixture to a bubbling simmer on the stovetop over medium-high heat. Once the broth is simmering, cover with the Dutch Oven lid and place in the oven and cook for 3 hours.
Whisk together the au jus gravy mix with one cup of water, add the mixture to the Dutch Oven, and cook another 1 1/2 hours.
Line a rimmed baking sheet with parchment paper.
Place the butternut squash cubes on the baking sheet and toss with the olive oil and seasonings.
Remove the roast from the oven and leave the lid on the Dutch Iven while you cook the squash.
Turn the heat up on the oven to 425 degrees F.
Place the butternut squash in the oven and roast for 30 minutes or until golden brown around the edges.
Serve the deer roast with the roasted butternut squash and a side of cooked white rice.