Start by slicing the bagels and preparing all your ingredients before cooking. Chop the green onions and jalapeños so everything is ready to go. Whisk the eggs with milk, salt, and black pepper in a bowl until smooth and slightly frothy.
Place a skillet over medium heat and add the chorizo sausage. Break it apart using a spatula while it cooks until browned and slightly crispy around the edges. Once fully cooked, transfer the sausage to a paper towel-lined plate to remove excess grease.
Using the same skillet, lower the heat slightly and pour in the whisked eggs. Stir slowly with a spatula so the eggs stay soft and fluffy. Cook just until set because the eggs will continue cooking slightly after removing them from the heat.
Spread butter lightly on the cut sides of the bagels before placing them in a toaster or skillet. Toast until golden brown and slightly crisp around the edges. Warm bagels hold the fillings better and add delicious crunch.
Place the scrambled eggs back into the skillet and top them with pepper jack cheese slices. Cover the pan for about a minute so the cheese melts evenly. The melted cheese creates a creamy layer that blends perfectly with the spicy sausage.
Spread cream cheese or jalapeño cream cheese on the toasted bagel halves. Add the cheesy eggs, cooked chorizo, sliced jalapeños, and green onions. Finish with hot sauce if desired, then close the sandwich and serve immediately.