Preheat your oven to 375°F (190°C). Lightly grease a 9x13 inch baking dish with olive oil or cooking spray.

Bring a large pot of salted water to a rolling boil. Add the ziti pasta and cook according to package directions until al dente (about 1 minute less than package suggests). Drain thoroughly and set aside.

While the pasta is cooking, heat olive oil in a large deep skillet over medium heat. Add the chopped onion and cook until softened and translucent, about 5 minutes, stirring occasionally. The edges should just start turning golden.

Add the minced garlic and chopped bell peppers to the skillet. Cook for another 5-7 minutes, or until the bell peppers are slightly softened but still have a bit of crispness. They should be tender enough to bite through easily.

Add the chopped zucchini and sliced mushrooms to the skillet. Continue to cook, stirring occasionally, until the zucchini is tender (easily pierced with a fork but not mushy) and the mushrooms have released their moisture and are starting to brown, about 8-10 minutes. The pan will look wet initially, then the liquid will evaporate.

Add the roughly chopped fresh spinach to the skillet. Cook until the spinach wilts completely, about 1-2 minutes. Stir in the Italian seasoning, red pepper flakes if using, salt, and black pepper.

Pour the marinara sauce into the skillet with the cooked vegetables. Stir well to combine. Bring the sauce to a simmer and cook for about 5-10 minutes, allowing the flavors to meld together. The sauce should coat the vegetables thickly.

In a large bowl, combine the cooked ziti pasta with about three-quarters of the vegetable marinara sauce. Toss gently to coat the pasta evenly.

Spread half of the sauced ziti mixture into the prepared baking dish. Using a spoon, dollop ricotta cheese in small mounds evenly over the ziti layer (about 10-12 dollops). Sprinkle about half of the shredded mozzarella cheese and half of the grated Parmesan cheese over the ricotta.

Top with the remaining sauced ziti mixture. Dollop the remaining ricotta cheese over the top layer in the same manner. Finally, sprinkle the remaining mozzarella and Parmesan cheese evenly over the ricotta. The top should be completely covered with cheese.

Cover the baking dish loosely with aluminum foil. Bake for 20 minutes. Remove the foil and bake for another 20-25 minutes, or until the cheese is melted, bubbly, and lightly golden brown on top.

Let rest for 10-15 minutes before serving. This allows the baked ziti to set slightly, making it easier to slice and serve cleanly.