Most of the events of the game usually involves bailing out one or more of your party.
Lance eventually leaves permanently at Watermin once he finds his father. Lily leaves once she finds love in Lance. Nell leaves to take control of his family's company after the fate of his parents is revealed (though he shows up once more at Diao to give Will a ride). And Eric leaves on Nell's plane and I don't know if he got back again. Kara's with you till the bitter end. And Seth, Hamlet, Nell's Parents, Some Random Guy, and Will's Parents show up for one last hurrah.
A couple of thoughts on the Inca Ship of Gold and some major plot spoilers of IoT:
I always thought that the Inca Queen and Will's mother were one and the same when I was a kid, but now that I think about it today, its more likely that she was a past incarnation of Will's mother since there was a lot of talk about the ring on her dusty boney husk of a finger which turned out to be the ring that allowed Kara into the Tower of Babel or something to that effect. They themselves were most likely dead before the sequence where you see them alive but what the player was supposed to infer was the fact that they couldn't move on without their king and Will's father was most likely a reincarnation of him while Will bore enough of a resemblance to pass as the King long enough to put the Inca spirits to rest.
Also I'm a goddamn idiot for not mentioning that the second spoiler tag in my previous post was about Secret of Mana. >.<