In a Dutch oven or large pot, saute the onion, fennel and garlic with the butter until the vegetables become soft (about 10 minutes). Add the red pepper flakes and saute the vegetables for a couple more minutes.
Add the tomatoes and 1/4 cup of water. Simmer over medium-low heat for 15-20 minutes covered with a lid.
In another medium size pot with a lid, heat the pot over high heat and add the mirin. Quickly add the clams. Cover with a lid and cook for about 6 minutes until all the clams have opened. Discard any that have not opened.
Transfer the clams to a separate bowl or plate and add about 1 1/2 cups of the clam juice to the pot of tomato sauce simmering. If you don’t have enough you can add water to get enough liquid to reach the right consistency. Mix to combine and transfer to a blender and blend until smooth. Pour the smooth tomato soup through a sieve back into the Dutch oven and add the clams back in.
Garnish with some fennel fronds and serve with bread and lemon wedges.