Arrange a rack to the middle and preheat the oven to 375º F.
Cook your pasta to al dente as per the instructions on the package; drain and set aside.
While the pasta cooks, heat a bit of olive oil in a skillet over medium-high heat. Add the diced onions and let them simmer until they've softened slightly—about two minutes. Add the mushrooms and green peppers, and let them cook until soft—about five minutes—stirring occasionally. Hit the skillet with a pinch of salt and a crack of pepper. Stir in the chopped pepperoni and, finally, add the noodles.
Gently toss the noodles to evenly distribute the cooked ingredients throughout. Add the marinara and freshly chopped oregano, and toss the pasta until it's evenly coated with sauce. Sprinkle the pasta with the mozzarella cheese, then top the cheese with slices of pepperoni, mushrooms, and green peppers.
Place the skillet in the oven, middle rack, and bake for about 15 minutes or until the cheese is fully melted. Then, turn on the broiler and broil the pasta skillet for about 5 minutes, or until the cheese is slightly golden and bubbly. If you're using cup n' crisp pepperoni, they should also be nicely curled up with crispy edges! (Best thing ever.)
Remove the pasta bake from the oven and let it sit for 5-10 minutes before digging in. It'll be difficult, I know. But it'll be worth the wait.