I tried a new method for these scrambled eggs: Cracking the eggs directly into the pan and 'scrambling' them once they were over the heat, then cooking them slowly. The result? Thick, luscious, and creamy eggs without any added cheese. It seems a little scary to scramble them in the pan, but trust me, it's worth it (and there's one less dish to clean). Eat the spinach-tomato mixture on the side (as pictured) or feel free to combine it with the eggs.
Add 1 tablespoon oil to a large pan over medium heat. When hot, add the onions, and cook, stirring occasionally until soft (but not browned), about 5 minutes. Then add the tomatoes and cook for 2 minutes more, or until the tomatoes start to soften a little. Add the spinach, tossing to combine with the onions and tomatoes until all the leaves are covered with a little oil and juice. Cook for another 5-7 minutes, until wilted and tender, seasoning with salt and pepper to taste. (If the spinach is done before the eggs, then bring the heat to low and partially cover to keep warm.)
Meanwhile, add the remaining oil to a small sauté pan over medium heat, adding the chile flakes if using. When hot, crack the eggs directly into the pan. Once all the eggs are in, immediately stir, breaking up the yolks. Season with salt and pepper, and lower the heat to medium-low. Cook for about 10 minutes, or until they've reached your desired level of doneness. Season for taste, and serve alongside, or mixed with the spinach-tomato mixture. Garnish with the thyme sprig, if using.