Heat a pot over medium high heat. Add the olive oil, onion, and garlic and sauté until the onion is translucent. Add the tomatoes, basil, oregano, red pepper flakes, and ½ t salt. Bring to a simmer and cook for 15 minutes.
In a bowl mix together the ricotta cheese, eggs, nutmeg, and ¼ t salt.
In a 9 x 13 inch by 2 inches deep baking dish, place 1 cup of the sauce. Begin the first layer by laying two sheets of pasta side by side to cover the bottom of the pan. Spread 1/3 of the ricotta mixture over the pasta, 1/3 of the remaining sauce over the ricotta, and then evenly spread 1/3 of the shredded mozzarella. Repeat 2 more times with the remaining ingredients but leave off the mozzarella on the top.
Take a knife and poke it through the lasagna layers evenly about every 2 inches. This will allow air to escape during baking and avoid big bubbles in the pasta. Cover and bake for 45 minutes.
Remove the cover and top with the remaining mozzarella cheese and bake for 15 minutes more. Remove it from the oven and let it rest for 20 minutes before serving. Serves 8-12.