Bring a large pot of salted water over medium heat to a boil. Add the linguine and cook until al dente.
Cook the bacon in a large saucepan, over medium heat, until crisp. Remove the bacon with a slotted spoon to a paper towel lined plate. Add the onions and garlic to the pan and saute until tender, roughly 3 minutes. Stir in the red pepper flakes, season with salt and pepper, to taste, and saute until fragrant. Add the heavy cream and simmer until thick, about 4 minutes, being careful not to burn the mixture. Stir in the cheese and lemon zest.
Drain the linguine and add to the saucepan. Carefully toss the pasta in the sauce. Add the bacon and season with salt and pepper, to taste. Transfer to a large platter and garnish with basil. Serve immediately while hot.