Start by cooking your brown rice according to the package directions. (Just a heads up, this will take at least 45 minutes.)
Place the butternut squash in a medium pot and add 3 cups chicken broth. Bring to a boil, then lower to a simmer, cover and cook for 20-25 minutes until very tender. Using a slotted spoon, transfer the butternut squash to a blender and puree until smooth. Reserve ¼ cup of cooking liquid. (You shouldn’t need to add any liquid to the blender, but if your blender is struggling, add a couple tablespoons of the cooking liquid to get things going.) Briefly set aside.
Pre-heat your oven to 375 degrees.
Heat the olive oil in a 10”-12” cast iron or ovenproof skillet over medium heat. When hot, add the onion, apple, sage, thyme and salt. Cook for 5-6 minutes until the onions are translucent and the apples have softened slightly. Add the sausages to the pan and cook for 6-8 minutes, breaking up the meat with a spatula, until no longer pink. Add the ¼ cup of reserved squash cooking liquid and cook for 1 more minute, making sure to scrape up any browned bits from the bottom of the pan.
Turn off the heat and stir the brown rice, butternut puree, and Fontina into the sausage mix. Taste the filling and season with a little extra salt if necessary.
In a small bowl combine the Panko and Parmesan. Smooth the top of the filling and sprinkle with the Panko mix. Bake for 25 minutes until lightly browned around the edges. Serve warm.