Time synchronization is an indispensable and fundamental requirement for all types of wireless sensor networks (WSNs) protocols and applications. The consistency and correctness of other protocols like localization, routing, etc., are highly dependent on time synchronization. However, due to the hostile deployment of wireless sensor networks, they are prone to cyber-physical attacks that create different threats to time synchronization protocols as well. Recently, consensus-based time synchronization (CTS) algorithms are gaining popularity due to their distributed nature and robustness toward different types of threats such as denial-of-service and node destruction. But, the inherent properties of the consensus-based approach of making in-network averaging make these algorithms vulnerable to message manipulation attacks. In this paper, an in-depth simulation-based analysis is conducted using pymote, a python-based discrete event simulator for WSN, on state-of-the-art CTS algorithms in the presence of message manipulation attacks. A novel and generic algorithm, Message Manipulation Attack Resilient CTS (MMAR-CTS) is proposed embedding which the state-of-the-art algorithms are extensively evaluated based on standard performance metrics, e.g., convergence speed, global synchronization error, and local synchronization error in the presence of the attack, and sufficient observations are derived to show the behavior of these algorithms. The comparison of protocols is validated with simulation results. Simulation results show that MMAR-CTS embedded SATS algorithm is 75% more efficient as compared to other candidate algorithms, measured in terms of convergence speed (number of iterations) and nearly 40% improvement in global and local synchronization error.