Bring a large pot of salted water to a boil and cook the pasta according to package instructions.
Reserve ½ cup pasta water, then drain the pasta and set aside.
Heat olive oil in a large skillet over medium heat.
Add the chopped onion and cook for 4–5 minutes until softened.
Stir in the minced garlic and cook for 1 minute until fragrant.
Add the crushed tomatoes and stir well. Let the sauce simmer for 5 minutes.
In a small bowl, whisk the miso paste with 2 tablespoons warm pasta water until smooth.
Stir the dissolved miso into the tomato sauce.
Add soy sauce, black pepper, and a splash of vegetable broth or pasta water.
Simmer for another 2–3 minutes until the sauce thickens slightly.
Add the cooked pasta to the skillet and toss until evenly coated.
Serve topped with fresh basil, Parmesan or vegan cheese, red pepper flakes, and a drizzle of olive oil.