Prepare your vegetables and measure out seasonings and set aside.
Cook your pasta in salted water until just before al dente. Reserve about ½ cup pasta water to thin sauce, if desired. Then drain and set aside until sauce is ready.
Using a large sauté pan on medium high heat, add olive oil and onions. Cook for 10-15 minutes until they start to brown. Stir occasionally and add a few dashes of water to help browning (without adding additional oil). browning the onions helps to bring out additional flavor.
Add in tomatoes and remaining ingredients. Cook sauce for another 10-15 minutes stirring occasionally. If desired use an immersion blender or regular blender to puree into a smooth sauce.
Once sauce has cooked, stir in shiso or basil if using. Taste for flavor, you can add a few teaspoons of sugar or honey to sweeten or a bit of shiokoji or soy sauce to make saltier. Add some freshly cracked pepper for an additional layer of flavor.
Combine with cooked pasta and cook another 1-2 minutes to finish cooking the pasta to desired consistency.