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Upon their arrival, Unmanned Autonomous Systems (UAS) brought with them many benefits for those involved in a military campaign. They can use such systems to reconnoiter dangerous areas, provide 24-hr aerial security surveillance for force protection purposes or even attack enemy targets all the while avoiding friendly human losses in the process. ...All this has the potential to turn the benefits of UAS into liabilities and although the last decade has seen great advances in the development of protection and countermeasures against the described threats and beyond the risk still endures. ...With this in mind the present work will describe a monitoring system whose purpose is to monitor UAS mission profile implementation at both high level mission execution and at lower level software code operation to tackle the specific threats of malicious code and possible spurious commands received over the vehicle's data links.