Step by Step method

1. Step 1.

   1.

2. Step 2.

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

3. Step 3.

   2.

4. Step 4.

   Stir in garlic and pepper flakes and cook until fragrant, about 30 seconds. Stir in tomato puree, water, and sugar and bring to a simmer. Reduce heat to medium-low and cook until flavors have melded, about 5 minutes. (Cooled sauce can be refrigerated for up to 3 days.)

5. Step 5.

   3.

6. Step 6.

   For the filling: Stir all ingredients in a bowl until thoroughly combined. Transfer filling to pastry bag or large zipper-lock bag (if using zipper-lock bag, cut 1 inch off one corner of the bag).

7. Step 7.

   4.

8. Step 8.

   For the shells: Adjust oven rack to middle position and heat oven to 400 degrees—place shells open side up on the counter. Pipe filling into shells until each is about three-quarters full. Divide the remaining filling evenly among the shells.

9. Step 9.

   5.

10. Step 10.

    Spread 1 cup sauce over the bottom of a 13 by 9-inch baking dish. Transfer shells, open side up, to prepared dish. Pour remaining sauce evenly over shells to completely cover.

11. Step 11.

    6.

12. Step 12.

    Cover dish tightly with aluminum foil and set on ra immed baking sheet. Bake until shells are tender and sauce is boiling rapidly, about 45 minutes. Remove dish from oven and discard foil; sprinkle fontina over top. Bake, uncovered, until fontina is lightly browned, about 15 minutes. Let shells cool for 25 minutes. Sprinkle with basil. Serve.