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First appeared in issue #2. An equally mysterious associate of Agent Graves, Joseph Shepherd was a former Minuteman who became their trainer and liaison with the Trust when he was appointed as its Warlord. He was ordered by the Trust to eliminate the Minutemen, but instead worked with Graves to conceal six of the seven that were present at Atlantic City. His true loyalties remained unknown as he maintained his own agenda somewhere between that of Graves' and the Trust's. Vying with Graves for control of Dizzy Cordova, Shepherd was mortally wounded when Wylie activated her, but he managed to appoint Lono as his successor and entrust him with Loop's training before succumbing to death in the desert somewhere near Juarez. He also cited Dizzy specifically as the replacement for Milo Garret, which suggests that Milo's death may have been manipulated more intentionally than previously thought.

In the Tarantula story arc, Mr. Shepherd's origin story revealed him to be a New York park basketball player who had served in Vietnam before being dishonorably discharged (it is implied for reasons related to his homosexuality). Agent Graves recruited Shepherd for the Minutemen after he was unable to prove Shepherd murdered a young man whom the story intimates had beaten another man into a coma. Graves was impressed by Shepherd after his own inability to prove the young man's guilt, as Shepherd seemed totally unrattled by any intimidation. Graves' decision to recruit Shepherd despite his homosexuality proved to be the last straw for Loop's father Curtis Hughes, who was excluded from the Minutemen because of his race, but had remained in service to Graves in the apparent hope that an exception would eventually be made if he proved himself capable and loyal.

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