SPOILER WARNING: Details about a quest, mission or other Final Fantasy XI in-game storyline follow.
In the present, he is only interacted with in Doll of the Dead, however he is mentioned many times in other missions. Zonpa is extremely arrogant and never hesitates to announce his name and title whenever the opportunity arises...which explains why his children hate him so.
He was imprisoned by the Ace Cardians just as the Great War ended, and has remained in a cell in The Boyahda Tree guarded by Mandragora ever since. He is presumed to be dead.