Preheat and prepare: Preheat oven to 400°F (200°C). Lightly oil a 9x13-inch (or similar) baking dish. Preheating ensures the dish goes into an already-hot oven so the top begins to brown quickly, giving you a crisp, attractive crust.

Season and sear the chicken: Pat the chicken breasts dry and season both sides with 1 tsp kosher salt and 1/2 tsp black pepper. Heat 1 tbsp olive oil in a large skillet over medium-high heat until shimmering. Sear the chicken 3–4 minutes per side until golden-brown (it will finish cooking in the oven). Browning creates the Maillard reaction — deep flavor and savory crust that intensifies the finished dish. Transfer chicken to a cutting board and let rest 5 minutes, then cut into 1/2-inch pieces.

Start the aromatics: Reduce heat to medium, add remaining 1 tbsp olive oil and 2 tbsp butter to the same skillet. When butter melts, add the diced onion and a pinch of salt and sweat for 4–5 minutes until soft and translucent. Add the minced garlic and cook 30–45 seconds until fragrant. Sweating onion and briefly toasting garlic releases their sugars and aromatic oils without browning, building a sweeter, layered base for the sauce.

Make a quick roux and creamy base: Sprinkle 2 tbsp flour over the softened onion and stir for 60 seconds to cook the raw flour taste and coat the aromatics. Slowly pour in 2 cups whole milk while whisking to avoid lumps, then simmer gently for 4–5 minutes until the mixture thickens into a light béchamel. This creates a creamy backbone that tames the acidity of the tomatoes and gives the bake a silky mouthfeel.

Temper the eggs and finish the sauce: In a small bowl, whisk 2 large eggs. Ladle about 1/2 cup of the hot milk mixture into the eggs while whisking constantly to temper (this prevents scrambling). Pour the tempered eggs back into the skillet and stir. Add 1 cup marinara, 1 cup spaghetti sauce, diced fresh tomato, 1 tsp Italian seasoning, and red pepper flakes if using. Simmer 2–3 minutes until everything is combined. The eggs enrich the sauce, adding body and a custardy silkiness when baked.

Taste and adjust seasoning: Taste the sauce and add salt and pepper to preference. Balancing acidity now (with a pinch of sugar, a splash of milk, or more salt) means the final baked dish will be perfectly seasoned rather than flat or overly tangy.

Cook the pasta al dente: Bring a large pot of salted water to a rolling boil. Cook the pasta until 2 minutes shy of package directions (about 7–8 minutes for most penne). Drain, reserving 1/2 cup pasta cooking water. Undercooking prevents the pasta from becoming mushy during the 20–25 minutes of baking; it will finish cooking in the oven while absorbing sauce.

Combine chicken, pasta and sauce: In a large bowl or the pot you used for pasta, add drained pasta, cut chicken, the creamy tomato sauce, 1 cup shredded mozzarella, and 1/3 cup grated Parmesan. If the sauce feels very thick, stir in up to 1/2 cup reserved pasta water to loosen — the starchy water helps the sauce cling to the pasta and keeps the bake moist.

Assemble in baking dish: Transfer the mixture to the prepared baking dish and spread into an even layer. Sprinkle the top with remaining mozzarella, the rest of the Parmesan, and a light grind of black pepper. A generous cheese topping ensures a golden, melty crust with a nutty finish from the Parmesan.

Bake until bubbly and golden: Bake uncovered at 400°F (200°C) for 18–22 minutes until the cheese is bubbly and beginning to brown. For a crisper top, switch to broil for 1–2 minutes — watch closely to avoid burning. Rest the bake 5 minutes out of the oven so the sauce sets slightly and is easier to serve.

Finish and serve: Scatter torn basil leaves over the top and serve hot. Resting and fresh herbs brighten and lift the rich flavors, giving the dish a final fresh pop.