Bring a large pot of salted water to a boil and cook the rigatoni according to package instructions until al dente.
While the pasta is cooking, heat 1 tablespoon of olive oil in a large deep skillet over medium-high heat.
Add the Italian sausage to the skillet, breaking it into small crumbles with a wooden spoon, and cook until browned and fully cooked (approximately 8 minutes). Remove sausage from the pan and set aside.
Add the remaining tablespoon of olive oil to the same skillet, then add the cubed butternut squash.
Sauté the squash for 8-10 minutes, stirring occasionally, until tender and caramelized on the edges.
Add the diced onion to the skillet and cook for an additional 4 minutes until translucent.
Stir in the minced garlic, fresh sage, and red pepper flakes; cook for 60 seconds until fragrant.
Pour in the chicken stock and heavy cream, using the spoon to deglaze the bottom of the pan.
Reduce heat to medium-low and simmer the sauce for 5 minutes until it thickens slightly.
Return the cooked sausage to the pan and stir in the Parmesan cheese until fully melted and incorporated.
Drain the pasta, reserving 1/2 cup of pasta water, and add the pasta to the skillet.
Toss the pasta with the sauce, adding reserved pasta water if needed to reach desired consistency. Season with salt and pepper before serving.