Preheat your oven to 400 degrees f.
Heat the oil in a large skillet, over medium heat. Add the onions and 1/4 cup of the broth. Cook, stirring occasionally until the onions are browned, and the liquid has evaporated.
Stir in the garlic and mushrooms, and continue to cook until tender, about 6-8 minutes more.
Meanwhile, season your chicken with sea salt and pepper, and dip it into the arrowroot or flour to lightly coat on both sides. Shake off any additional.
Once the veggies are done, set them aside on a plate.
Melt the butter/ghee in that same skillet over medium heat. Add the chicken in 2 separate batches and cook until golden on both sides, around 8-10 minutes in total.
Transfer the chicken to a large baking dish and top with your sauteed veggies.
In that same skillet (do not wipe it out as we want the dry bits to flavor and thicken this sauce), stir in the marsala wine and the remaining broth. Bring to a high simmer, stirring through the bottom of the pan to deglaze. Allow the sauce to simmer for around 5 minutes to thicken up, then pour it over the chicken and veggies.
Top with your freshly shredded cheese and bake in your preheated oven for about 15 minutes, or until bubbly and the cheese is melted. A meat thermometer inserted into the thick part of each chicken should read 165 degrees f.
Garnish with chopped parsley, and red pepper flakes then enjoy!