Spray a 9x13-inch baking dish with nonstick spray.
Spread the tomato paste in the bottom of the baking dish. Stir in water, olive oil and chopped onion. Season with salt and pepper.
Wash and very thinly slice eggplant, zucchini, squash, yellow bell pepper, and red bell pepper.
Arrange vegetables in rows, make sure each vegetable is overlapping another one. Order doesn’t mater.
Once the roasted garlic is done, remove from oven and grab the bottom of the garlic head and gently squeeze until the cloves pop out into the pie dish- they will be mushy. Take a fork and mash with 1/4 cup fresh basil, 1/4 cup parmesan, 1 Tablespoon olive oil, and crushed red pepper flakes. Rub mixture all over the top of the prepared vegetables.
Drizzle 3 Tablespoons over vegetables, sprinkle with fresh thyme leaves, and season with salt and pepper.
Cover with parchment paper or foil and bake in over for 45 minutes.