Instructions

1. Arrange a rack in the middle of the oven and heat the oven to 400°F. Lightly coat a 9x13-inch baking dish with 1 tablespoon of the olive oil.
2. Bring a large pot of salted water to a boil. Add 1 pound dried penne pasta and cook until al dente, about 1 minute less than package instructions. Meanwhile, finely chop 8 ounces cremini mushrooms, 1 small shallot, and 2 garlic cloves. Finely chop 2 ounces of the pepperoni. Grate 8 ounces mozzarella cheese on the large holes of a box grater (about 2 cups).
3. When the pasta is ready, reserve 1 cup of the pasta water. Drain the pasta, then return to the pot.
4. Heat the remaining 2 tablespoons olive oil in a large skillet over medium-high heat until shimmering. Add the shallot, mushrooms, and garlic, and cook, stirring occasionally, until the shallots are translucent and the mushrooms are starting to brown, about 3 minutes. Add 1 tablespoon Italian seasoning, 1 teaspoon red pepper flakes if using, 1/2 teaspoon kosher salt, and 1/2 teaspoon black pepper. Cook until fragrant, about 1 minute. Add the chopped pepperoni and cook for 1 minute more.
5. Add the mushroom mixture to the pot. Add 1 (about 24-ounce) jar marinara sauce and reserved pasta water and stir to combine. Taste and season with more kosher salt as needed.
6. Transfer half the pasta mixture to the baking dish and spread into an even layer. Sprinkle with half of the cheese. Top with the remaining pasta. Sprinkle with the remaining cheese, then top with the remaining 2 ounces sliced pepperoni in a single layer.
7. Bake until the cheese is bubbling and starting to brown, 20 to 25 minutes. Let cool for about 10 minutes before serving.