Jonathan doesn't know the others very well, but he's closer to Bjorn than any other. He couldn't care less about beating the League, aside from perhaps taking the money to fund his other exploits, but rather adventures to find more about Ghost-type pokemon, and where they come from. He's particularly interested in Yamask, since it's the one ghost-type pokemon with a solid link to deceased humans. Aside from this, he also likes Psychic-type pokemon, though to a lesser degree. He particularly likes the Unown, and aside from solving the secret of the Ghosts, one of his greatest dreams is to explore the Solaceon Ruins.
His father has been missing for as long as he can remember; he used to be a trainer planning on taking on the Pokemon League, before mysteriously disappearing. The police suspect Team [REDACTED]'s involvement, but they've been unable to prove anything. His mother shares many of Jonathan's eccentricities, though she tends more towards Dark pokemon than Ghost-types. She used to be a pokemon breeder, before deciding to take up a more mundane job at the Pokemart to spend more time raising Jonathan after his father disappeared.
He knows the other players primarily due to simply running into them when going out to buy books. The only one whose companionship he actively seeks out is Bjorn, with whom he's become fairly friendly. He does consider the others good acquaintances. His closest friend by far, however, is his Gastly, Shub-Niggurath (Shub for short). He found him long ago when the Gastly came into his room while he was young. While other children of that age would be terrified, he instead offered it an Oran berry. The Gastly returned a few times after that, with Jonathan giving it berries each time it visited. Eventually, it began to follow him around, at which point his mother invested in a pokeball for it.