Command and control (C2) paths for issuing commands to malware are sometimes the only indicators of its existence within networks. Identifying potential C2 channels is often a manually driven process that involves a deep understanding of cyber tradecraft. Efforts to improve discovery of these channels through using a reinforcement learning (RL) based approach that learns to automatically carry out C2 attack campaigns on large networks, where multiple defense layers are in place serves to drive efficiency for network operators. In this paper, we model C2 traffic flow as a three-stage process and formulate it as a Markov decision process (MDP) with the objective to maximize the number of valuable hosts whose data is exfiltrated. The approach also specifically models payload and defense mechanisms such as firewalls which is a novel contribution. The attack paths learned by the RL agent can in turn help the blue team identify high-priority vulnerabilities and develop improved defense strategies. The method is evaluated on a large network with more than a thousand hosts and the results demonstrate that the agent can effectively learn attack paths while avoiding firewalls.