In a large skillet over medium-heat heat, add half of the olive oil, and sear the Italian sausage until golden brown on all sides. Remove from the skillet and set aside.
Preheat oven to 350°F, and place ramekins on a baking sheet. In the same skillet where you seared the sausage, add the remaining olive oil, followed by the mushrooms and onions. Season with Italian seasoning, salt, and some of the red pepper flakes, and cook until mushrooms are softened and onion is translucent. Set aside.
In the ramekins, start with a layer of marinara sauce, then add a sprinkle of fresh basil (if using). Layer with mozzarella cheese, parmesan, pepperonis, Italian sausage, mushrooms, and onions, then repeat the layers. The last two layers should be mozzarella cheese, pepperonis, and basil.
Bake for 15-20 minutes until cheese is bubbly and golden. Remove from the oven, and garnish with more red pepper flakes, parmesan, and fresh basil. Enjoy!
Store in the fridge for up to 5 days in airtight containers, or the ramekins covered with plastic wrap, aluminum foil, or tops to the ramekins.