As modern systems become larger and the impact of a failure can be wide-ranging in some cases causing havoc to everyday life system reliance, the ability of a system to withstand major disruption and to recover within an acceptable time frame, becomes increasingly important. While systems failures can have many causes, component faults and cyber intrusions are two common such causes which can occur separately or one type can cause another failure of the other type. In this monograph, the authors describe in detail the research on fault diagnosis, opacity analysis and enhancement, and cyber security analysis and enforcement, within suitable discrete event system modelling frameworks. In each case, they describe basic problem statements and key concepts, and then point out the key challenges in each research area. Finally the authors present a thorough review of state-of-the-art techniques, and discuss their advantages and disadvantages. This monograph is a thorough overview of the cutting edge of research on resilient systems. It will be starting point for the readers own research into improving the reliability and fault-tolerance of modern-day engineering and computer systems.