Prepare vegetables by dicing onion, shallot and red pepper. Cut fennel bulb into half-moon slivers, and fine dice garlic.
Once vegetables are prepared, add 2 tablespoons olive oil to a dutch oven over medium-high heat. Add in diced onion and shallot, stirring to cook for about 5 minutes, until soft and translucent.
Stir in diced red bell pepper and cook for another 3 minutes or so, careful not to burn vegetables. Toss in minced garlic and fennel bulb slivers, and cook for another 1-2 minutes.
Add in 4 cups vegetable broth, clam juice and crushed tomatoes. Once the broth begins to boil, add in bay leaf, parsley, oregano, red pepper flakes (optional), salt and pepper.
Reduce heat to medium-low to simmer, and stir in tomato paste. Let simmer for about 20 minutes. While broth is simmering, prepare seafood.
Clean mussels, removing beards and rinsing thoroughly, discarding any ones with cracked shells. Peel and devein shrimp, if needed, leaving tails on (optional). Cut cod into chunks about the same size as shrimp, or approximately 1-inch cubes.
Once broth has been prepared, return heat to medium-high and add in mussels. Put a lid on the pot to allow steam to help mussels open up. This should take about 7-10 minutes.
After mussels have opened, remove lid and add cod chunks and shrimp, stirring to combine. Cook for about 5 minutes, until cod is cooked through.
Serve.