Preheat oven to 375°F.
For the dipping sauce, heat a small saucepot over medium-high heat with 1 turn of the pan of EVOO, about 1 tablespoon. Add the onions, pepper and crushed red pepper flakes, and cook; stirring every now and then until soft, about 4 minutes. Add the fire-roasted tomatoes and season with salt and pepper. Bring up to a bubble and simmer the sauce for about 10 minutes.
Once you have the sauce going, unravel the pizza dough onto a lightly floured surface and stretch to make an even rectangle. In an even layer, on half of the rectangle, place the pepperoni down leaving a 1-inch border and sprinkle with the mozzarella cheese.