Heat the olive oil in a large pot over medium heat. Sweat the fennel, onions and garlic, stirring frequently, until softened, 8 to 12 minutes. Add the white wine and reduce the liquid by half. Add the clam juice and bay leaves. Bring to a boil, then reduce the heat and simmer for 20 minutes. Strain the stock and discard the solids. Set aside the stock.
Clam Spaghetti
Bring a large pot of heavily salted water to a rapid boil. Cook the pasta according to package instructions.
Heat the olive oil in a large skillet with a lid over medium heat. Add the garlic and sweat for 1 minute. Add the clams and some of the clam stock (you may not require all of it, depending how saucy you like your pasta), and cover immediately. Keep covered until the clams are fully open, 3 to 4 minutes; discard any that remain closed. Add the cooked spaghetti, butter and chili flakes and cook for a few more minutes. Adjust with more clam stock if needed. Add the parsley, lemon juice, scallions and jalapeno and toss well to combine. Season with salt as needed and serve.
Notes
Always make sure to choose very fresh clams and "purge" them to get rid of all possible sand: flush them in ice-cold salted water (2 tbsp salt per 4 cups), changing the solution two or three times during the process.