1. Cook pasta salted water for the minimum cooking time suggested, approximately 5 minutes. Drain and set aside.
2. In a pan, swirl a bit of olive oil in a pan and add garlic and onions. Cook down, stirring occasionally, until onions soften.
3. Add beef to pan with salt, nutmeg and red pepper flakes. Cook meat until almost completely browned, approximately 5-7 minutes. Take off the heat.
4. Spray a 9 x 13 baking dish with cooking spray and press pasta down on bottom layer. Top with cooked beef mixture then tomatoes.
5. In a small bowl, mix cottage cheese with eggs and spread over the tomatoes.
6. Layer the spinach leaves, followed by red peppers then mushrooms. Alternate zucchini and squash in rows on the very top. Tuck the basil leaves in between the zucchini and squash pieces.
7. Sprinkle the cheddar and mozzarella on top and cover with aluminum foil. Bake in a preheated oven at 375 degrees for 35 minutes. Raise oven heat to 450, remove foil and bake another 5-10 minutes or until bubbly and cheese browns slightly. Allow to rest at least 10 minutes after taking it out of the oven. Sprinkle with extra basil.