Step 1

For the sauce: Heat the oil in a large saucepan over medium heat until shimmering. Add the onion, salt, and pepper and cook, stirring occasionally, until softened and lightly browned, about 10 minutes.

Step 2

Stir in the garlic and red pepper flakes and cook until fragrant, about 30 seconds (don’t brown the garlic). Stir in the crushed tomatoes, water, and sugar and bring to a gentle boil. Reduce the heat to medium-low and cook, uncovered, until flavors have melded, about 5 minutes. (The cooled sauce can be refrigerated for up to 3 days.)

Step 3

For the filling: Stir all the ingredients in a medium bowl until thoroughly combined. Transfer the filling to pastry bag or large zipper-lock bag, and cut ½-inch off of the tip or corner of the bag. (If using a zipper-lock bag, be sure the corners are square; the rounded-corner bags are difficult to use.)

Step 4

For the shells: Adjust the oven rack to middle position and preheat the oven to 400°F. Place the shells open side up on the counter. Pipe the filling into shells until each is full.

Step 5

Spread 1 cup of the sauce over the bottom of 9x13-inch baking dish. Transfer the shells, open side up, to the prepared dish. Pour the remaining sauce evenly over the shells to completely cover.

Step 6

Cover the dish tightly with aluminum foil. Bake until the shells are tender and the sauce is boiling rapidly, about 45 minutes. Remove the dish from the oven and discard the foil; sprinkle the fontina or mozzarella over top. Return to the oven and bake, uncovered, until the cheese is lightly browned, about 15 minutes. Let the dish cool, uncovered, for 15 to 20 minutes (this rest is essential to fully cook the pasta). Sprinkle with the basil and serve.