In a pan, add the onion and sauté until soft, about 5 minutes.
Add the garlic and cook for a further 30 seconds.
Add in the chicken and cook till it is slightly brown.
Stir in the chipotle, chilli flakes, salt and pepper.
Cook till the chicken is cooked and the sauce has evaporated
Place a tortilla on a plate.
Spread 1 tbsp of red sauce on the tortilla
Fill half the tortilla with some of the cooked chicken, tomatoes, capsicum, cheddar and mozzarella.
Fold into half and place this on a pan over medium heat.
Cook until the tortilla is crisp and golden and the cheese is melted, adjusting the heat as necessary, a few minutes per side.
Repeat with the remaining tortillas.
Let the quesadillas rest a few minutes to allow the filling to set, then cut into wedges.
Mix the sour cream with some cilantro and serve this by the side.