I've played it both ways with Yoshimo betraying you (btw he leaves without giving back any of the cool stuff you may have outfitted him with.) He claims that Irenicus would have killed him if he didn't betray you. The second time through I had Volgyar instead of Yoshimo in the party. I dropped him to pick up Imoen and to the best of my knowledge he spent the rest of his days in the mind maze of the Asylum waiting for my return (poor sap...already finished his quests). But to answer your question the pirate captain puts the sleeping powder into your soup if Yoshimo is not in the party.
Did anyone else notice that you don't get the experience points for quest solved if you walk into the Asylum with the ward stone versus having the pirate king commit you?
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