Cook the pasta according to package instructions in a pot of boiling salted water.: You will smell the starchy steam rising as the pasta softens and the water returns to a lively boil, and that bubbling sound signals proper doneness. Stop cooking when the pasta still has a slight bite; it will finish in the oven and you want each piece to hold its shape and texture. A common error is leaving the pasta in until completely soft which makes the final casserole mushy instead of al dente. If your pot is crowded it will take longer to return to a boil, so use a large pot and high heat to keep the water rolling.
Preheat oven to 375°F.: You will notice the oven light warming the interior and a steady heat settling in when it reaches temperature. Having the oven fully warmed ensures the casserole starts baking immediately and the cheese melts evenly. Skipping preheating can cause uneven bake times and a soggy center, because the dish needs consistent radiant heat to bubble through. Use an oven thermometer if your oven runs cool or hot, as inaccurate temperatures affect texture and browning.
In a large skillet, heat olive oil over medium heat. Add the chicken and season chicken with salt and pepper. Cook the chicken until no longer pink, about 5 minutes.: You will hear a soft sizzle as the pieces hit the oil and see color develop along the edges, that caramelization gives savory depth. Cook until the interior is opaque and juices run clear, flipping pieces as needed to brown evenly. Rushing this step by using too high heat can char the outside while leaving the center undercooked, so keep a steady medium and give pieces space to brown rather than steam.
Add the butter to skillet and melt. Stir in onions and cook for 3 to 5 minutes until the onion soften and become translucent. Add garlic and saute for another 30 seconds until aromatic.: The butter will foam and coat the pan, softening the onion into sweet translucency which balances the tomatoes. When the garlic hits the warm pan you will smell a bright, savory perfume almost immediately, a sign to move quickly. Overcooking the garlic will turn it bitter, so add it after the onion has softened and stir only briefly until fragrant.
Season with more salt and pepper if needed, then add the oregano, basil, and red pepper flakes. Stir in the chicken broth and bring to a boil, scraping all the brown bits. Add crushed tomatoes and simmer for 5 minutes.: The moment you add the chicken broth , you will see steam and hear a more vigorous simmer as the browned bits lift from the pan, creating a rich base. The dried herbs will bloom in the hot liquid, releasing savory aromatics that marry with the acidity of the tomatoes. Simmering concentrates the sauce so it clings to ingredients; rushing this stage leaves a watery mouthfeel. Watch for a gentle rolling simmer and stir occasionally to prevent sticking and to integrate flavors evenly.
Transfer the cooked pasta to a 9×13-inch casserole dish, pour chicken tomato sauce over the pasta and a cup of the mozzarella cheese, then toss well. Sprinkle the remaining mozzarella cheese over the top of the casserole.: The steaming pasta will release a faint aroma of wheat as you move it into the casserole dish, and coating it with the sauce ensures each piece carries flavor. Toss gently so sauce envelops the pasta without crushing it, folding in a cup of shredded Mozzarella cheese to start a creamy internal layer. Avoid piling the pasta in clumps; distributing sauce evenly prevents dry pockets and ensures uniform melting in the oven.
Transfer the casserole dish to the oven and bake for about 15 to 20 minutes, just until the cheese melts and gets bubbly.: As you scatter the shredded Mozzarella cheese , it will create a pale blanket that soon turns glossy and bubbly. The top layer browns lightly and forms that irresistible pull when served. Too little cheese will leave the surface uncohesive, while too much can make the casserole overly heavy. Aim for even coverage so the heat can lift and brown the entire top uniformly.
Transfer the casserole dish to the oven and bake for about 15 to 20 minutes, just until the cheese melts and gets bubbly: You will hear a faint pop as pockets of steam escape and see small bubbles appear around the edges before the entire surface becomes glossy. This short bake finishes melding flavors and warms the dish through without drying it out. Leaving it in too long will tighten the cheese into a drier crust, while pulling it out too early means the cheese is not fully melted and the center may be underheated. Check visually for bubbling and a lightly golden top as your cue to remove it.