Bring a large pot of salted water to a boil and cook the pasta until just al dente, about 1 minute less than package instructions. Drain and set aside.
Preheat your oven to 180°C (350°F). In a large mixing bowl, combine the cooked pasta, marinara sauce, chopped vegetables, dried oregano, basil, and half of the nutritional yeast. Mix everything until well coated and evenly distributed.
Pour the pasta mixture into a 9x13 inch baking dish, spreading it out evenly with a spatula or spoon.
Sprinkle the remaining nutritional yeast and a pinch of salt and pepper over the top for a cheesy, flavorful crust.
Place the dish in the oven and bake uncovered for 25-30 minutes, until the top is golden brown and bubbling around the edges.
Remove from the oven and let sit for 5 minutes — this helps the sauce thicken and makes serving easier.
Garnish with freshly chopped basil or herbs if desired, then serve hot for a comforting, cheesy vegan meal.