In a 6 qt or larger pot over medium heat, sauté shallot, fennel, and red pepper flakes in a nice splash of olive oil. Season with a fat pinch of salt and some black pepper. Cook for 10 minutes.
Add garlic to pot and cook another 2 minutes. Then add tomato paste and cook an additional 2 minutes.
Pour in wine and stock. Add tomatoes one by one, breaking them apart with your hands. Careful, they're squirters! Pour in remaining juice from tomato can. Throw in capers and lemon zest.
Cover and raise heat to bring to a boil, then immediately reduce to a simmer, cover, and let flavors make out for 30 minutes.
When 30 minutes are up, pour in beans with their juices. Bring back to a simmer.
Add mussels and cover. Cook just until mussels have opened.
Add calamari and shrimp and simmer gently until shrimp are just cooked through, about 5 minutes. Give it a nice stir and season to taste with salt and pepper.
Ladle cioppino into bowls and garnish with fresh basil and fennel fronds. Serve with crusty bread (I like to heat mine in the oven until toasted!).
BUON APPETITO!