Cut a lengthwise 3/4-inch thick slice from each zucchini. With a spoon, scoop out the flesh, leaving a shell intact all around the zucchini. Discard or save the flesh for another use. Chop up the long slices of zucchini.
Heat the olive oil in a skillet over medium heat, and cook the chicken sausage, breaking the meat up as it cooks, until the sausage has begun to brown, about 8 minutes.
Sprinkle in the crushed red pepper flakes, and season with salt and black pepper. Stir in the chopped zucchini, onion, and garlic, and cook until the onion is translucent, about 5 minutes. Scrape the sausage mixture into a bowl, and stir in the tomatoes, bread crumbs, Parmesan cheese, and basil until the stuffing is thoroughly combined.
Lightly stuff the zucchini boats with the stuffing, place the zucchini into a baking dish, and bake until thoroughly heated through and beginning to brown on top, about 30 minutes.
