Spray a 9x13-inch baking dish with cooking spray and arrange bagel pieces in an even layer.
Distribute cream cheese cubes, cooked sausage, cheddar cheese, red onion, and scallions evenly over the bagel pieces.
In a large bowl, whisk together eggs, milk, 2 tablespoons of everything bagel seasoning, and black pepper until well blended.
Pour egg mixture over the casserole, making sure to coat everything evenly. Press down lightly to ensure bagel pieces absorb the liquid.
Sprinkle remaining 1 tablespoon of everything bagel seasoning on top. Cover and refrigerate for at least 4 hours or overnight.
Preheat oven to 350°F. Bake covered with foil for 30 minutes, then uncover and bake for an additional 20 minutes until golden and set in the center. Let rest for 10 minutes before serving. To freeze, cool completely, wrap tightly in plastic wrap and aluminum foil, and freeze for up to 3 months. Thaw in refrigerator overnight and reheat at 325°F for 30-35 minutes.