He was there in end of the Suns and lovers and then all of a sudden disappeared from the show.
I'm guessing this was in part due to the actors commitments or whatever, but was it ever explained later in the seasons? (if this results in a spoiler, please use tags accordingly).
Jothee left after season three when he and Ka D'Argo fell out over their mutual (and undisclosed) relationship with Chiana. All three of them were having emotional difficulties and this led to their eventual disbanding of their family unit.
He would not return until the Peacekeeper War Miniseries. He would leave D'Argo to become a member of the Luxan Army and would rescue Chiana and D'argo when their ship was destroyed by the Scarrans. Achieving the title of Kleeva, D'Argo and Jothee reconciled before D'Argo was killed protecting Chiana. D'Argo bequeathed his Qualta Blade to his son and this was carried out by Chiana.
As far as the actor was concerned there was a recasting of the role:
The young Jothee who appeared in Season 1 was portrayed by Grant Magee. In his short story arc in Season 2 and 3, Matthew Newton was cast. For the miniseries, Nathaniel Dean took over the role. He is one of only a few returning characters over the history of Farscape to be recast.
