Within the context of delegating separation related tasks from an air traffic controller to the flight deck, this paper analyzes the merging and spacing problem for autonomous aircraft operations at busy airway intersections. A consensus-based control protocol is developed to achieve an ordered and safe traffic flow at a given intersection waypoint. Two primary implementation steps are covered in the protocol. In the first step, consensus on the target merging flow is achieved, where the merging stream is modeled as a straight line with the minimum total converging distance. In the second step, multiple aircraft with double-integrator dynamics and time-varying communication topologies are guided to merge into the target flow while maintaining appropriate interaircraft spacing. A state control law is designed, and the Lyapunov analysis method is leveraged to derive sufficient conditions on the communication topology and the control parameter for merging agents to reach consensus in finite time. Performance of the proposed method is evaluated through experimental simulations under different hypothetical scenarios in the two-dimensional plane.