- "Poor creatures. Why must we destroy you? I'll tell you why. Order is the tide of creation. But yours is a species that worships the one over the many. You glorify your intelligence. Because it allows you to believe anything. That you have a destiny. That you have a right. That you have a cause. That you are special. That you are great. But in truth, you are born insane. And such misery cannot be allowed to spread!"
- —A Control Bug-infected Shepherd[src]
United Citizen Federation
At some point, Shepherd became the leader of 701st Mobile Infantry. Five years after the Klendathu System Campaign, during the battle of ZA, he led an invasion and his unit personally on the ground, followed by Intel psychic lieutenant Pavlov Dill and Bravo Six. However, the battle ended in disaster with Federation in retreat. Shepherd gets cut off with a large portion of his force. Survivors retreat to Hotel Delta 1-8-5 where they hold out awaiting retrieval. Unknown to them, three stragglers they had picked up had been infected with Control Bugs.
After two days waiting for retrieval, Shepherd and his soldiers were infected by the Control Bugs. Now under the control of the Control Bug instead of his own free will the general tried to kill or infect the last two of his uninfected Troopers. Simultaneously Shepherd attempted to escape Hotel Delta 1-8-5 on a DR-8 Skyhook so as to get to the Federation's high command and defeat the Federation from inside. Infected Shepherd nearly escaped Hotel Delta 1-8-5, but Captain Dax shot him several times killing the Infected General and preventing the Control Bugs' plans.
Before being infected by the Control Bug, he was a charismatic leader, who valued the lives of his troopers, which was shown during his admonishment of Pavlov Dill, informing the Psychic Officer to discuss with him how the majority of his troopers were killed.