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This paper builds upon the foundation and clarifies specifications for a necessary security protocol in Wireless Sensor Networks (WSNs) with cooperative communications. It is designed to enhance performance and resiliency against cyber-attacks. Recent literature has shown that developing a WSN with Cooperative Communication greatly increases the performance of the network, but also exposes new vulnerabilities. The technique operates by transmitting packets of data to neighboring relay nodes in a cooperative fashion to reach the destination. In this paper, we consider security issues in WSNs with cooperative communication on each layer of the OSI model: physical layer, data link layer, network layer, service (topology) layer, and application layer. For each layer, we clarify the main task, enumerate the main attacks and threats, specify the primary security approaches and techniques (if any), and discuss possible new attacks and problems that may arise with the use of cooperative communications. Furthermore, we show for some attacks (e.g., jamming, packet dropping, and wormhole) that using cooperative communication improves the network resiliency and reliability. Finally, we propose a security protocol that addresses many of these shortcomings, while outlining the remaining issues that need further work and research.