In a bowl, whisk the eggs with salt and pepper until they are well blended.
Spray a skillet with cooking spray and cook the green peppers, tomatoes, and onions until softened.
Add the eggs in the skillet and cook over medium heat until the eggs and veggies are cooked thoroughly.
In a separate skillet, warm the tortilla over medium heat, flipping often.
When the pan and tortilla are warm, sprinkle cheese ½ of the tortilla. Top the cheese with scrambled eggs and your mix-ins. Then top that with more cheese, and fold the tortilla in half.
Let the quesadilla cook until golden brown, about 2 minutes, Then filp and cook the second side until golden and crispy (about 1-2 minutes).
Immediately remove from the heat and transfer to a cutting board to cool and cut.
Serve immediately with salsa, sour cream, etc.