Unmanned Aircraft Systems (UAS) are forcing a rethink on how traditional safety and security assessment processes are conducted. Traditional concerns have been with the safety and security of the crew and passengers on the aircraft, but with the advent of UASs, these shift to the risks that the system presents to people and infrastructure on the ground, and other air users. This shift is presenting challenges to a large body of stakeholders, including: the rulemakers, the UAS designers, the operators, safety and security assessors and the regulators. This paper provides a case study focussing on the command and control link to the aircraft, and describes the challenges experienced and developments made. Also, as a test case the paper aims to lay down a framework for a generalised approach for the harmonious integration of safety and security disciplines.