For the Sauce
Process tomatoes and their juice through food mill, pulse in food processor until puréed, or purée with immersion blender. Purée should not be completely smooth, but should have no chunks larger than 1/16th of an inch. Set tomatoes aside.
Combine oil and butter in medium saucepan and heat over medium-low heat until butter is melted. Add garlic, oregano, pepper flakes, and large pinch salt and cook, stirring frequently, until fragrant but not browned, about 3 minutes. Add tomatoes, onion halves, basil sprigs, and sugar. Bring to a simmer, reduce heat to lowest setting (bubbles should barely be breaking the surface), and cook, stirring occasionally, until reduced by half, about 1 hour. Discard onions and basil stems. Season to taste with salt. Allow to cool and store in covered container in the refrigerator for up to 2 weeks.
For the Pie
Combine flour, sugar, salt, and yeast in bowl of food processor. Pulse 3 to 4 times to incorporate. Add water and olive oil. Run food processor until mixture forms ball that rides around the bowl above the blade, about 15 seconds. Continue processing 15 seconds longer.
Transfer dough ball to lightly floured surface and knead once or twice by hand until smooth ball is formed. It should pass the windowpane test. Divide dough into three even portions and place each in a covered quart-sized deli container or in a zipper-lock freezer bag. Place in refrigerator and allow to rise at least 1 day, and up to 5.
At least two hours before baking, remove dough from refrigerator and shape into balls by gathering dough towards bottom and pinching shut. Flour well and place each dough ball in a separate medium mixing bowl. Cover tightly with plastic wrap and allow to rise at warm room temperature until roughly doubled in volume.
One hour before baking, adjust oven rack with pizza stone to middle position and preheat oven to 500°F (260°C). Turn single dough ball out onto lightly floured surface. Gently press out dough into rough 8-inch circle, leaving outer inch higher than the rest. Gently stretch dough by draping over knuckles to form a 12- to 14-inch circle about 1/4-inch thick. Transfer to pizza peel.
Spread approximately 2/3 cup sauce evenly over surface of crust, leaving 1/2- to 1-inch border along edge. Evenly spread 1/3 of cheese over sauce. Slide pizza onto baking stone and bake until cheese is melted with some browned spots and crust is golden brown and puffed, 12 to 15 minutes. Transfer to cutting board, slice, and serve immediately. Repeat with remaining two dough balls, remaining sauce, and remaining cheese. |