Preheat oven to 350 degrees.
Spread zucchini, squash, and eggplant in a single layer on a baking sheet. Drizzle with the olive oil. Season with salt and pepper. Roast in the oven for 20 minutes until vegetables are tender. Set vegetables aside.
In the meantime, cook sausage in a large skillet over medium high heat. Break sausage up into bite-sized pieces with a spoon and continue to cook until sausage is no longer pink.
Add garlic to the skillet and cook until fragrant, about 30 seconds.
Add cream cheese and stir until melted.
Add tomato sauce and fresh basil. Add roasted vegetables and stir until everything is well-combined.
Spread half of the mixture into the bottom of a prepared 9 x 13-inch casserole dish. Layer with half of the pepperoni then half of the mozzarella cheese. Repeat with the remaining sausage/vegetables mixture, pepperoni, and cheese. Sprinkle Parmesan over the top of the casserole.
Bake for 20 minutes or until cheese is melted. Let casserole stand for 10 minutes before serving.