Bring a large pot of lightly salted water to a boil. Cook linguine at a boil until tender yet firm to the bite, about 11 minutes; drain.
Heat a skillet over medium heat; cook and stir onion and bacon until onion is tender and bacon is crisp, about 6 minutes. Add scallops, garlic, red pepper flakes, black pepper, and salt; cook and stir until scallops are cooked through, about 1 minute. Stir in wine; cook for 1 minute.
Remove skillet from heat and stir parsley into scallop mixture. Top linguine with scallop mixture and garnish with lemon zest.