In a medium saucepan over medium-high heat, cook bacon until just beginning to crisp. Remove bacon from pan and drain on paper towels. Leave bacon fat in pan.
Add butter to saucepan and melt over medium heat. Add flour and whisk to combine. Continue cooking, stirring, for about a minute. Slowly pour in milk, whisking as your pour, to create a smooth sauce. Reduce heat to medium and cook, stirring frequently, until thickened enough to coat the back of a spoon. Turn off heat, add cheese, and stir until melted. Taste and season with salt and pepper.
Combine hot cheese sauce with cooked pasta and reserved bacon until pasta is warmed through. Top with toasted panko and fresh chives. Serve hot.
