Preheat oven to 400º. Lightly grease 18 muffin cups. In a small skillet, melt butter over medium heat on stovetop. Sauté onion until tender; set aside. In a large bowl, whisk together eggs, milk, chives, and pepper. Stir in cheese, crumbled bacon, crumbled English muffins, and cooked onion. Spoon batter into prepared muffin cups. Bake for 20 minutes. Let cool in cups for 5 minutes before removing.
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