Shepherd was an SG team leader, and led Gus Bonner's first missions. He taught Gus things such as to think for himself and to be ready to do whatever was neccessary.
During one of their missions, the team's rookie, Swallow, stepped on some sort of alien thing that stung his foot and went right through his boot. When they got the boot off, his foot swelled to the size of a pumpkin. Just as the guy was about to faint, Shepherd told him that he has ugly feet anyway.
At some point, Gus started disagreeing with him all the time, so Shepherd had him transferred to another team.
Eventually, Harley retired and didn't tell anyone about it, so he appeared to be missing to the SGC.
When Shepherd arrived on the Mostari's world, he saw that the natives were starving and their villages were feuding with each other. Shepherd introduced plows, crop rotation, medicine, as well as adapted the English alphabet and taught them to read. He wrote laws for them and brought them order. He ended up becoming the people's ruler.
In the 2020s, Major Gus Bonner's team visited his planet. They witnessed Mostari rebels going against Harley's rule, while other Mostari would grovel to Harley when he would pass by them. They also saw that the natives had built a statue of him and a house.
Gus saw Shepherd as a hero and couldn't see how he had gone too far with becoming the people's ruler, however, Gus's niece Stacey could tell and convinced him otherwise.
During their visit, Shepherd was told that Da'kyll was after Bonner's team because they believed Draga was an Ancient. Later, he made a deal with the Tlak'kahn to let them have Draga but to let the others go, however, he was lied to, as Da'kyll was going to eliminate Gus and the other humans anyway. He told him the deal was off but Da'kyll refused and reminded him that they only let him live on his world because he is occasionally useful to them and that he better do what he's told if he wants to keep protecting his planet. When the Ancient wasn't found, Da'kyll blamed Shepherd and decided he had outlived his usefulness. He told him if Gus Bonner escapes, he won't.
During the fight between Bonner's team and the Tlak'kahn, Shepherd ordered Zucca to hide the Mostari in the forest until the Tlak'kahn left. He then joined Bonner's team. His house was then burned down.
He told the Mostari that he had to leave and make up for the things he had done. His last order was to tell the Mostari to think for themselves for now on and make their own decisions, and after the Tlak'kahn are gone, they can build their own world. He then had Ec'co activate the stargate. Bonner noticed he was traveling light and Harley told him that it would be a nice change and mentioned he might have been carrying too much baggage with him when he arrived to the Mostari's world. Bonner offered that he come with them but he told him he and the Mostari didn't need him anymore. He went through the gate to a place where nobody would mistake him for a hero. (INF: "Mentor")