Heat a large Dutch oven or soup pot with a lid over medium heat. Add the olive oil, diced fennel and onion and season with salt and pepper. Cover and cook until the vegetables are tender, about 4 minutes. Add the garlic and red pepper flakes and cook until fragrant, 1 minute more. Add the wine and simmer until most of the liquid is reduced, about 5 minutes. Add the tomatoes with their juice and simmer, uncovered, until the liquid is reduced by half, about 5 minutes.
Add the lobster stock and bring to a simmer. Add the clams, cover and cook until the clams just begin to open, about 5 minutes. Once the first clam opens, add the cod, scallops and mussels and cover. Once the mussels open, the rest of the seafood should be cooked through and opaque, about 3 minutes. Season with salt and pepper and sprinkle with the reserved fennel fronds.
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