Mobile Ad hoc Network (MANET) is the significant technology among various wireless communication technologies where all the nodes are mobile and which can be connected to dynamically used wireless link in a random manner. They connect or disconnect from the active network any time and transfer packets in a single or a multicast mode. Nodes are connected by way of wireless links and form a random topology. This research paper focuses on, performance comparison of a new Intrusion Detection Systems (IDS), Secure-Enhanced Adaptive 3 Acknowledgement with hybrid cryptography's EA3ACK-MARS4 and EA3ACK-ECC specially designed for MANET. Furthermore, all the above mentioned protocols are compared based on several important performance metrics which are Packet Delivery Ratio (PDR), end-toend delay and average energy via one of the efficient networking routing protocol called Network Simulator 2 (Ns2). It is used to implement and test the suggested system under various size of topology with different constant sets of nodes as well as comparing the results with two different protocols.