In a large baking dish, combine the onions, oil and thyme. Bake until the onions are golden and tender, stirring occasionally, about 40 minutes.
Stir the bell pepper strips and vinegar into the onion mixture. Season with salt and pepper and push to one side of the dish. Season the fish with salt and pepper and arrange alongside the vegetables.
Bake until the fish is opaque, about 10 minutes. Transfer the swordfish to a platter and arrange the vegetables over the top.