In a large deep skillet or sauté pan on stove, heat oil over medium high. Add the onions and a pinch of salt, stirring often until soft, about 4 minutes. Add the garlic and cook for another minute. Increase the heat to high and add the ground meat. Cook until browned all the way through.
Add the chipotle peppers, tomatoes, cumin, paprika, salt, pepper, cayenne, nutmeg, cilantro, and feta and stir well with the other ingredients. Reduce to medium heat and cook the tomato mixture until slightly thickened.
Make 6 indentations into the skillet mixture with the back of a large spoon. Crack each egg into an indentation. Cover and cook for 5 to 7 minutes, or until both the egg whites and yolks are fully cooked. Drizzle with the honey and sprinkle with cilantro, scallions, and jalapeno chili. Serve with garlic naan, Greek yogurt, and hot sauce.