Cook pasta according to package directions. Drain and set aside.
Melt butter in saucepan over low heat; whisk in flour, and cook, whisking constantly, 1 minute or until mixture is smooth. Increase heat to medium; gradually whisk in 2 cups milk, and cook, whisking constantly, 5 minutes or until mixture is thickened and bubbly. Stir in cheese, stirring until cheese is melted. Remove pan from heat.
Stir pasta, and ground black pepper into cheese mixture; spoon into a lightly greased 13 x 9 inch baking dish. Spread crushed Cheez-it crackers on top.
Bake uncovered at 375°F for 30 minutes or until thoroughly heated.