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Preheat the oven to 375 degrees.
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Bring a large pot of salted water to a boil. Cook pasta according to package instructions.
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In a skillet, melt butter. Now whisk in flour until dissolved. Cook for 1 minute.
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Add in tomato paste and stir to combine. Now, add milk, salt, oregano, and red pepper flakes. Whisk until smooth and simmer for 2 minutes.
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Mix in half the cheese and drained pasta. Top with pepperoni and remaining cheese.
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Bake for 10 minutes, or until everything is brown, bubbly, and golden.
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Serve and enjoy! :D