Preheat oven to 350F and place a large pot of salted water over high heat to boil for the pasta.
Place a large, oven-safe skillet over medium-high heat with the EVOO. Add the scallions, parsley and fennel seeds to the pan and cook until the scallions are tender, about 1 minute. Add the white wine and let it cook about 1 minute until most of the liquid is reduced away.
Add the diced tomatoes and clam juice to the pan along with the fish, some salt and freshly ground black pepper. Bring the liquids up to a bubble, and then put a lid on the pan (or some aluminum foil if you don't have a lid) and transfer it to the oven. Bake until the fish is cooked through, 15-20 minutes.
When the fish has about 5 minutes of cooking time left, drop the pasta into the boiling water and cook to al dente according to package directions. Once it has finished cooking, drain the pasta and reserve it in the colander until the sauce is finished.
When the fish has finished cooking, remove it to a plate and cover it with foil to keep warm. Return the pan of sauce to the stove over medium-high heat and bring up to a bubble. Simmer until some of the liquid has reduced away, 2-3 minutes.
While the liquids are reducing, stir together the softened butter with the flour in a small bowl. Toss the mixture into the pan and whisk to combine to thicken the sauce. Stir in the balsamic vinegar, cream and basil, and remove the pan from the heat.
To serve, pour half of the sauce over the fish and toss the cooked pasta in the remaining half.