Step 1

Thinly slice about 2 pounds yellow onions (about 6 cups). Heat 2 tablespoons of the olive oil in a large skillet over medium-low heat until shimmering. Add the onions and cook, stirring every 8 to 10 minutes, until they are caramelized and jammy, 45 to 50 minutes total. Meanwhile, cook the pasta, make the sauce, and prepare the remaining ingredients.

Step 2

Arrange a rack in the middle of the oven and heat the oven to 375°F. Coat a rimmed baking sheet with 1 tablespoon of the olive oil. Bring a large pot of heavily salted water to a boil. Add 30 dried jumbo pasta shells and cook until al dente, 8 to 9 minutes. Drain the pasta well. Transfer to the baking sheet and arrange into a single layer.

Step 3

Grate 6 ounces Parmesan cheese on the smallest holes of the box grater (about 2 cups), or measure out 2 cups store-bought grated; transfer half to a large bowl and the remaining half to a medium bowl. Grate 8 ounces Gruyère cheese on the large holes of a box grater (about 2 cups).

Step 4

Trim and thinly slice 1 medium bunch scallions (about 1 cup). Transfer half to the medium bowl and the remaining half to the large bowl.

Step 5

Melt 4 tablespoons (1/2 stick) unsalted butter in a medium saucepan over medium heat. Add 1/4 cup all-purpose flour and stir constantly until light brown in color, about 2 minutes. Add 1 1/2 cups whole milk, 1 1/2 cups beef broth, and 2 teaspoons Worcestershire sauce, and whisk to combine. Bring to a simmer, then simmer until thick enough to coat the back of a spoon, about 5 minutes.

Step 6

Add the Gruyère and stir until melted. Remove the saucepan from the heat. Taste and season with salt as needed.

Step 7

Thinly slice 3 large garlic cloves (about 1 tablespoon). Pick the leaves from 6 fresh thyme sprigs until you have 1 tablespoon; add half to the medium bowl. When the onions are almost ready, add the garlic and remaining thyme and cook for 5 minutes more.

Step 8

Add the caramelized onions, 1 (15 to 16-ounce) container ricotta cheese, and 3/4 teaspoon of the black pepper to the large bowl and stir to combine. Taste and season with salt as needed.

Step 9

Add the remaining 2 tablespoons olive oil, remaining 3/4 teaspoon black pepper, and 1/2 cup panko breadcrumbs to the medium bowl and stir to combine.

Step 10

Assemble the stuffed shells: Pour half of the cheese sauce (about 1 1/2 cups) into a 9x13-inch baking dish and spread into an even layer. Stuff the onion mixture into the shells with a spoon (about a heaping tablespoon in each) and place them filling-side up in the dish. (Alternatively, transfer the filling into a zip top bag, cut off a bottom corner, and pipe the filling into the shells.)

Step 11

Spoon the remaining cheese sauce evenly over the shells. Sprinkle evenly with breadcrumb mixture.

Step 12

Bake until the breadcrumbs are golden brown and the sauce is bubbling, 30 to 35 minutes. Let cool for 10 minutes before serving.