
Preheat oven to 400℉ (205℃). Cook pasta shells according to the instructions on the package.
While the shells are cooking, heat a large skillet over medium heat. Cook the ground beef until evenly browned, 2-3 minutes.
Add the onions, garlic, Italian seasoning, thyme, tomato paste, ½ cup of spaghetti sauce (reserving the rest), salt, and pepper to taste. Simmer for 2-3 minutes, and add the fresh basil and spinach. Cook until wilted.
When the shells and the meat sauce are ready, place the shells face up into a large baking dish. Stuff 1½ tablespoons of meat mixture into the opening of each shell.
Spoon the reserved spaghetti sauce on top.
Mix the mozzarella cheese and Parmesan and sprinkle it on top. Bake for 15 minutes or until the cheeses melt and start to brown.
Remove from heat and let the stuffed shells rest for about 5 minutes. Garnish with parsley if desired. Serve hot.