Bring a large pot of lightly salted water to a boil. Cook spaghetti in boiling water, stirring occasionally, until tender yet firm to the bite, about 12 minutes.
Meanwhile, heat 2 tablespoons olive oil in a large skillet over medium heat and cook onion until golden brown, about 5 minutes. Add pancetta and cook, stirring occasionally, until crisp, 2 to 3 minutes. Pour in passata, water, and sugar; cook until sauce has thickened, 10 to 15 minutes.
Drain spaghetti and toss with sauce, remaining olive oil, Parmesan cheese, and red pepper flakes. Season with salt and pepper.
