Heat a large skillet over medium heat. Chop the bacon, sausage, or ham and add to the skillet, cooking until crisp. Remove the grease.
Crack the eggs into a bowl and add a splash of water or milk. Whisk until smooth.
Add eggs to the skillet and season with salt and pepper. Cook over medium heat, scrambling into small pieces, until desired doneness.
Cover one flour tortilla with a thin layer of shredded cheese. Top with some of the scrambled eggs and bacon, ham, or sausage.
Top with some more shredded cheese and place another flour tortilla on top.
Carefully set the quesadilla into a pan over medium heat. Cook until the cheese begins to slightly melt and the bottom of the tortilla is golden brown.
Carefully flip to the other side and cook for 1-2 minutes. Remove to a plate.
Slice and serve warm with salsa and/or sour cream.