Preheat the oven to 425 °. Heat the olive oil in a large enameled cast-iron casserole.
Add the onion, leek and garlic, cover and cook over low heat, stirring occasionally, until softened, about 10 minutes.
Add the wine and cook until almost evaporated, about 3 minutes. Add the squash, Swiss chard, red and yellow bell peppers, fennel seeds, thyme and crushed red pepper.
Season the vegetables generously with salt and pepper, cover and cook over low heat, stirring occasionally, until the squash is tender, about 15 minutes.
Spread half of the vegetable stew in an 8-by-11-inch glass or ceramic baking dish.
Season the halibut with salt and pepper and nestle the fillets in the stew; cover with the remaining vegetables.
Bake for about 15 minutes, or until the halibut is just cooked through. Sprinkle with the basil and serve.