Toss your chopped bacon into a large skillet over medium-high heat and let it cook for about 4 to 5 minutes, stirring occasionally, until it's crisp and browned. Move it to a plate lined with paper towels so the extra grease drains off. I usually leave a little bacon fat in the pan since it adds so much flavor to the vegetables that go in next.
In the same skillet, warm your olive oil (or leftover bacon grease) over medium heat and add the onion, tomato, and jalapeño. Cook for about 4 to 5 minutes, stirring now and then, until everything softens and smells fragrant. This step builds the flavor base for the whole filling, so don't rush past it.
While your veggies cook, whisk the eggs with milk, salt, and pepper in a bowl until fully combined. Pour the mixture into the skillet with the vegetables and cook over medium-low heat, stirring gently, until the eggs are just set but still soft. Pulling them off the heat a touch early keeps them from turning rubbery.
Stir the crispy bacon back into the egg and veggie mixture, then remove the skillet from the heat. Give everything a light toss so the filling is evenly combined. This is the moment where all those separate components turn into one cohesive, savory mix ready for the tortilla.
Lay a tortilla flat and sprinkle cheese over one half, then spoon a portion of the egg filling on top of the cheese, and finish with another light layer of cheese. Fold the tortilla in half, pressing gently so the filling stays put. Repeat with the remaining tortillas and filling.
Melt a little butter in the skillet over medium heat and place the folded quesadilla in the pan. Cook for about 2 to 3 minutes per side, pressing down lightly with your spatula, until both sides are golden brown and the cheese has fully melted. Slice into wedges and serve while it's hot.