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Cook pasta al dente according to package directions. Remove one cup water then drain pasta.
Heat olive oil over medium high heat. Add onions and sauté for 4 minutes. Add squash and sauté an additional 4 minutes. Add garlic and red pepper flakes and sauté 30 seconds.
Add water, bouillon and all remaining seasonings/spices. Bring to a boil, cover and reduce to a simmer. Simmer until squash is fork tender, about 8-12 minutes. Add to blender (or use an immersion blender) and puree until smooth being careful to let some steam escape so the lid doesn’t explode (I cover a corner with a paper towel.
Add butternut squash puree back to pan. Heat through then stir in 1/2 cup Parmesan until smooth. Add pasta and toss to coat, adding additional Reserved Pasta Water to reach desired consistency.
Garnish with additional freshly grated Parmesan, bacon and toasted pine nuts.