This dissertation investigates vulnerabilities in unmanned vehicles and how to successfully detect and counteract them. As we entrust unmanned vehicles with more responsibilities (e.g. fire-fighting, search and rescue, package delivery), it is crucial to ensure their safe operation. These systems often have not been designed to protect against an intelligent attacker or considering all possible interactions between the physical dynamics and the internal logic. Robust control strategies can verify that the system behaves normally under bounded disturbances, and formal verification methods can check that the system logic operates normally under ideal conditions. However, critical vulnerabilities exist in the intersection of these fields that are addressed in this work. Due to the complex nature of this interaction, only trivial examples have previously been pursued. This work focuses on efficient real-time methods for verification and validation of unmanned vehicles under disturbances and cyberattacks. The efficiency of the verification and validation algorithm is necessary to run it onboard an unmanned vehicle, where it can be used for self diagnosis. We begin with simple linear systems and step to more complex examples with non-linearities. During this progression, new methods are developed to cope with the challenges introduced. We also address how to counter the threat of unmanned aerial systems (UASs) under hostile control by developing and testing an estimation and control scheme for an air-to-air counter UAS system.