Toast the bagel halves until golden brown and set aside.
Heat the vegetable oil in a medium skillet over medium heat.
Add the onions and jalapeños to the skillet and sauté for 5 to 7 minutes until the onions are caramelized and jalapeños are softened.
Push the vegetables to the side of the skillet and add the pastrami slices, searing for 1 minute per side until the edges are crispy.
In a small bowl, whisk the eggs with salt and pepper.
Melt the butter in a separate non-stick skillet over medium-low heat and pour in the whisked eggs.
Cook the eggs undisturbed for 2 minutes until the base is set, then fold the edges inward to form a square shape that fits the bagel.
Place the cheese slice over the eggs, cover the skillet with a lid, and turn off the heat to allow the cheese to melt for 1 minute.
Place the egg and cheese on the bottom bagel half, then layer the warm pastrami followed by the sautéed onions and jalapeños.
Top with the remaining bagel half and serve immediately.