Preheat the oven to 400 degrees F. Rinse the tomatoes and then place them in a single layer in 9x13 baking dish. Drizzle with 2 Tbsp. of olive oil, add the garlic cloves, and sprinkle with the Kosher salt and cracked black pepper. Tomatoes will roast for about 45 minutes.
In an 8-quart stockpot on medium-high heat, add the remaining olive oil and chopped onions and sautee until tender. Then add the red pepper flakes, canned tomatoes, thyme, and vegetable broth.
Add the roasted tomatoes and garlic, including the liquid from the dish, to the pot. Stir well then bring to a boil and simmer for an hour. Let this cool completely then process in the blender, adding fresh basil before pureeing.
Return soup to the stockpot or a Crock Pot to keep warm, or fill freezer-safe containers.
Recipe adapted by Brandi Koskie from Ina Garten