Heat the olive oil to a large saute pan or skillet over medium-high heat. Add the onions and saute for about 5 minutes until softened but not completely translucent.
Add the zucchini, season with salt and pepper, and cook, stirring occasionally, for about 15 to 20 minutes more until the zucchini is very tender but not mushy.
Meanwhile, bring a large pot of water to a boil. Generously salt the water and add the pasta. Cook until al dente, reserve ½ cup of pasta cooking water and then drain the pasta.
Add the zucchini and onion mixture to a blender or food processor and add the ½ cup reserved pasta water, fresh basil, and cheese. Puree until smooth and adjust seasoning as needed. You should have about 3 ½ cups sauce.
Mix about 3 cups of the zucchini sauce with the cooked pasta until well-coated, adding more sauce as needed.
