Cook the bacon in a large, deep skillet over medium-high heat until crisp, about 10 minutes. Remove the bacon with a slotted spoon and drain on a paper towel-lined plate; return the skillet with the reserved bacon grease to the stove.
Cook the onion in the bacon drippings until soft, 5 to 7 minutes. Stir in the green beans and red pepper flakes; cook another 2 minutes. Pour the boiling water into the skillet and cover the skillet immediately; steam for about 15 minutes, shaking the skillet occasionally to keep the beans from sticking to the bottom. Add the butter, lemon juice, salt, and pepper; cook and stir until the butter is melted, 3 to 5 minutes. Sprinkle the cooked bacon over the beans to serve.