Preheat your oven to 450°F (230°C).

Bring salted water to a boil in a large pot for the penne pasta.

In a large bowl, combine diced butternut squash, plum tomatoes, and yellow onion. Drizzle with olive oil and sprinkle salt, black pepper, fresh thyme, and red pepper flakes. Toss until coated.

Spread the seasoned vegetables on a baking sheet and roast for 20-30 minutes, stirring halfway through.

Cook the penne pasta according to package instructions until al dente. Reserve ½ cup of pasta water before draining.

Transfer the roasted vegetables to a blender, adding the reserved pasta water, and blend until smooth and creamy.

Toss the creamy sauce with the cooked penne pasta in a large bowl. Serve with a drizzle of olive oil and a sprinkle of grated Parmesan cheese if desired.