John's relationship with his brother, Hal, is one of great trust and respect. The brothers lost their father when John was still a boy; consequently, Hal acts as a fatherly elder brother, looking after John while helping him make his own way. After their father's death, John lived away from home and Hal for two years, staying with his mother's people in Aberdeen. Even after John had returned to England, the brothers did not interact much, as Hal was busy building up the regiment. During the campaign against the Scottish Jacobites in 1745-6, John accompanied Hal and his regiment to the Highlands, where John had his first taste of military life and warfare. It was there, after the Battle of Culloden and the death of John's friend and lover, Hector, that Hal explained that John must see his friend's body, in order to accept his death, grieve him, and move on.
John took up his commission with Hal's regiment, the 46th, and since then the brothers have grown closer, sharing their talent for soldiering.
On the matter of John's sexuality, Gabaldon has suggested that Hal almost certainly knows of John's preference for men, but that the brothers would never speak of it. She has hinted that even if Hal wasn't directly responsible for John's exile to Ardsmuir (in the wake of a near-scandal involving George Everett), he almost certainly had a hand in it.
↑Gabaldon, Diana. "The Custom of the Army (SPOILERS!)." MSG: 66876.109. Diana Gabaldon. Books and Writers Community. Compuserve. Published 27 March 2010. Accessed 18 July 2016.