Preheat oven to 400°F. Cut stems off tomatoes. Roast on a rimmed sheet pan until soft, 35 - 40 minutes.
Heat the oil in a large skillet over medium-high heat. Saute onions until soft. Add garlic and cook for 1 more minute. Add tomatoes with any pan juices, chipotle peppers, cumin, oregano, salt, pepper and stock to the pan, Bring to a simmer and cook for 2 - 3 minutes.
Carefully pour the hot sauce mixture into a blender or food processor. Pulse until smooth. Pour back into the skillet, bring to a simmer and cook for 10 minutes until thickened. Add salt, pepper to taste.
Cool sauce in the pan. Use right away or transfer to airtight container and refrigerate for up to 1 week. Or freeze for up to 3 months.