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In Baldur's Gate II: Throne of Bhaal Balthazar is found acting as the de facto ruler of Amkethran, living in the monastery with his monks while his mercenaries live in and largely control the town outside. Since he's so focused on achieving his ultimate goal, he has let the town's populace to fall into poverty, and the dishonorable mercenaries run amok amongst them, bullying them at their leisure. Balthazar's ultimate goal is to destroy all other Bhaalspawn and, at the end, commit ritual suicide – he believes death is bred in the bones of his kind so deeply that they will always bring destruction regardless of intention, and that destroying them all is the only way to do away with Bhaal's essence. As such, he's not very different from the other Five in his cooperation with the rest, since they all more or less intend to destroy each other to increase their own power. It is to this end that he sees it as necessary to gather an army of his own in form of the mercenaries, just like all the others save maybe Illasera. He works with Melissan without trusting her.
After the destruction of Saradush, Melissan advises the player character's party to travel to Amkethran and meet her there. Once there, they will meet with Balthazar who claims that she has left already. The player will next need to use Amkethran as a base in hunting down Sendai and Abazigal, but once that is done, Elminster will appear and reveal a number of things. It will turn out that Balthazar is a Bhaalspawn himself and that he had a hostile confrontation with Melissan, who has fled. The player must next return to Amkethran, make their way through a town full of hostile mercenaries, and enter the monastery with Saemon Havarian's help. There they will confront Balthazar and learn of his true motives. The ensuing conversation can only end in violence, even if Balthazar acknowledges that the player character's intentions are honourable.
Note: One of the many mods done to the Baldur's Gate series of games allowed for the player to fight Balthazar again or recruit him into his or her group to fight the remaining bhaalspawn & Melissan. Though this mod is not considered canon in Forgotten Realms history is still available.
Balthazar also appears in the novelization.