A multi-agent network system consists of a group of dynamic control agents which interact according to a given information flow structure. Such cooperative dynamics over a network may be strongly affected by the removal of network nodes and communication links, thus potentially compromising the functionality of the overall system. The chief purpose of this thesis is to explore and address the challenges of multi-agent cooperative control under various fault and failure scenarios by analyzing the network graph-topology. In the first part, the agents are assumed to evolve according to the linear agreement protocol. Link failures in the network are characterized based on the ability to distinguish the agent dynamics before and after failures. Sufficient topological conditions are provided, under which dynamics of a given agent is distinguishable for distinct digraphs. The second part of this thesis is concerned with the preservation of structural controllability for a multi-agent network under simultaneous link and agent failures. To this end, the previously studied concepts of link and agent controllability degrees are first exploited to provide quantitative measures for the contribution of a particular link or agent to the controllability of the overall network. Next, the case when both communication links and agents in the network can fail simultaneously is considered, and graphical conditions for preservation of controllability are investigated.