Preheat the oven to 190˚C. Lightly grease a large casserole dish, approximately 23 cm in diametre.
Cook the penne according to packet instructions until tender. Drain and cover.
While the pasta is cooking, fry the bacon in a pan over medium heat for about 3 minutes. Add the onion and red pepper and sauté until the onion is just starting to soften, but not brown. Toss the tomatoes in the pan briefly, then add this mix to the pasta.
Stir 2/3 of the cheese into the pasta. Pour the pasta into the casserole dish and use your hands to make sure the add-ins are evenly distributed.
Whisk the eggs in a large bowl and season with salt and pepper. Pour the eggs over the pasta and shake the dish to make sure the egg is evenly distributed. Top with the remaining cheese.
Bake for 25 to 30 minutes or until the cheese is bubbling and melted. Garnish with chives and serve warm. Leftovers can be reheated in the microwave or oven at low temperature.