Bring a large pot of salted water to a rolling boil. Cook the spaghetti until just barely al dente — about two minutes less than the package directions suggest. It will continue cooking in the oven, so you don't want it fully soft at this stage.

Drain and toss lightly with a drizzle of olive oil to prevent sticking. Set aside.

While the pasta cooks, heat olive oil in a large skillet over medium-high heat. Add the diced onion and cook for about three minutes until it softens and turns translucent.

Add the garlic and stir for another 30 seconds until fragrant.

Add the ground beef, breaking it apart with a wooden spoon. Cook until fully browned with no pink remaining, about 6 to 8 minutes. Drain any excess fat.

To the skillet with the browned meat, add the marinara sauce, drained diced tomatoes, Italian seasoning, salt, pepper, and red pepper flakes if using. Stir everything together.

Let the sauce simmer over medium-low heat for about five minutes to allow the flavors to meld. Taste and adjust seasoning as needed.

Preheat your oven to 375°F. Lightly grease a 9x13-inch baking dish.

Add the cooked spaghetti to the meat sauce and toss well so every strand gets coated. Transfer the mixture into the prepared baking dish and spread it out evenly.

Sprinkle the shredded mozzarella evenly over the top, followed by the Parmesan cheese.

Cover the dish tightly with aluminum foil and bake for 20 minutes.

Remove the foil and bake for another 10 to 15 minutes until the cheese is golden, bubbly, and just starting to brown at the edges.

Let the baked spaghetti rest for five minutes before serving to allow it to set for clean slicing and serving.