Heat oil in a large pot over medium heat. Add fennel and shallots and cook until soft and translucent, 6 minutes. Add garlic, oregano, and red pepper flakes and season with salt and pepper. Cook until fragrant, 1 minute more.
Add wine and let boil until reduced by half, 3 to 5 minutes, scraping up browned bits with a wooden spoon. Add tomatoes, clam juice, water, bay leaves, and orange zest (if using). Stir to combine, bring to a low simmer, and cook, stirring occasionally, for 20 minutes.