In a large skillet, heat 3 tablespoons of extra-virgin olive oil over medium-low heat. Add the diced onion and grated garlic. Sauté for about 2–3 minutes, stirring occasionally, until the onion begins to soften and the garlic becomes fragrant. Be careful not to let the garlic brown, as it can become bitter.

Reduce the heat to low and arrange the halved Roma tomatoes in the skillet skin-side up, with the cut side resting directly against the bottom of the pan. Arrange them in a single layer as much as possible. Cover the skillet with a lid and allow the tomatoes to gently cook for 10–15 minutes, or until they become very soft and tender.

Check the tomatoes by gently pressing them with a fork. When the skins begin to loosen and can be easily pulled away, the tomatoes are ready. Carefully remove and discard the skins using a fork or a pair of tongs. Don't worry if a little skin remains—the sauce will still turn out beautifully.

Add the thyme, oregano, parsley, crushed red pepper flakes, salt, black pepper, and heavy cream to the skillet. Stir gently to combine all of the ingredients.

Using an immersion blender, carefully blend the tomato mixture directly in the skillet until the sauce is completely smooth and creamy. Move the blender around the skillet to ensure all of the tomatoes are incorporated.

Alternatively: Carefully transfer the hot mixture to a countertop blender. Remove or loosen the blender's center cap to allow steam to escape, cover the opening with a kitchen towel, and blend carefully until smooth. Work in batches if necessary and use caution when blending hot liquids.

Once the sauce is smooth and creamy, a tomato puree, reduce the heat to low and gradually stir in the 2 cups of freshly grated Parmesan cheese. Continue stirring until the Parmesan is completely melted and incorporated into the sauce. If the sauce is thicker than you'd like, gradually add reserved pasta water, a few tablespoons at a time, until you reach your desired consistency.

Taste the finished sauce and adjust the salt, pepper, or crushed red pepper flakes as needed. If serving with pasta, toss the sauce with your warm pasta and add a little reserved pasta water as needed to help the sauce coat the noodles.

This recipe makes approximately two batches of tomato sauce. Enjoy one batch immediately and allow the remaining sauce to cool completely before freezing. Transfer the extra sauce to a 1-quart freezer-safe mason jar, leaving some space at the top for the sauce to expand as it freezes. Seal tightly, label with the date, and freeze for future meals. Thaw the sauce in the refrigerator before reheating gently on the stovetop.