Start by preheating your oven to 400 degrees. Add the cubed butternut squash to a baking dish, season with salt and pepper, and drizzle with olive oil.
Bake for 30 minutes until fork tender, and let cool.
Cook your pasta just before al dente, drain and set to the side.
Heat a large skillet on medium heat, and then add in the butter. Let the butter sizzle and bubble and get a light brown, then add in the pasta and squash. Gently toss, and cook for a minute or two.
Add in the sage, chili flakes, and parmesan cheese, and give another good toss. Cook for a few more minutes until the cheese slightly melts, then serve. Add a few cherry tomato slices to cut through some of those flavors, if you desire.