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Orpheus is revealed to be inside the Astral Prism at the very beginning of Act 3 and becomes a pivotal plot point surrounding Raphael, his desire for the Crown of Karsus, and the Emperor. The choice just before the final battle eventually becomes whether to side with the Emperor or free Orpheus in order to take on the Netherbrain. However, when it comes time to free Orpheus, a strange thing can occur which makes no sense: once the Emperor leaves and if the player doesn't want to become a full illithid, then Orpheus will quickly transform into one.
Orpheus is revealed to be inside the Astral Prism at the very beginning of Act 3 and becomes a pivotal plot point surrounding Raphael, his desire for the Crown of Karsus, and the Emperor. The choice just before the final battle eventually becomes whether to side with the Emperor or free Orpheus in order to take on the Netherbrain. However, when it comes time to free Orpheus, a strange thing can occur which makes no sense: once the Emperor leaves and if the player doesn't want to become a full illithid, then Orpheus will quickly transform into one.
Immediately after he is freed from his chains, Orpheus will begrudgingly confirm that the Emperor was correct. The party's previous attempt to subdue and control the Absolute failed because the Elder Brain had been changed by the Crown into a Netherbrain, and only an illithid can take it down. With the Emperor gone, the choice now falls to the party to either give up one of their own to fully transform or for the newly released githyanki prince to become his own worst nightmare.
The choice itself is not necessarily the plot hole, although it does fall into the category of being obvious plot logic designed to throw one final choice at the player. And perhaps an illithid mind is truly needed to out-think the Netherbrain and ensure victory. But it does seem more than a little odd that despite Orpheus clearly being able to hold off the Absolute's influence even when not fully conscious, he suddenly can't defeat it now without transforming.
Even if an illithid was needed to defeat the Netherbrain by staying two steps ahead, that still doesn't explain the larger Orpheus plot hole: his immediate transformation. The choices of the Emperor, Tav, or Karlach make sense, as one is already a Mind Flayer while the other two have a tadpole each, or multiple if illithid powers have been used. However, there is no indication that Orpheus had been infected, making his metamorphosis a little confusing.
After muttering that the Netherbrain would be eager to claim him, Orpheus will kneel on the ground and just change. It's a strange and jarring scene that seems to completely disregard all the established rules for ceremorphosis. A single line with him requesting an Astral Tadpole from the party or mentioning a prior infection would have solved this, but instead the party are left to watch as Orpheus apparently wills himself into a Mind Flayer.
It would have been far more interesting, as well as make more sense, to have Orpheus act as the true alternative to the Emperor. This way, he could have provided the same role in the final battle but just not as an illithid. If Orpheus isn't transformed, then his Way of the Four Elements monk abilities are on offer to the party as they travel to the Netherbrain, which, given the mental fortitude of monks, would still have made sense for him to dominate the Netherbrain.
Having Orpheus not transform without the need to sacrifice a party member could have offered a clearer "good" Baldur's Gate 3 ending, but also have fit with the characters of the Emperor and Orpheus better. If Orpheus is sided with, then the Emperor leaves to join the Netherbrain, which is a bizarre choice given how much effort he's put into remaining free and maintaining control of his own mind. The Emperor's betrayal feels oddly reminiscent of Dragon Age 2's controversial second final boss, where even if the mages were sided with, First Enchanter Orsino would still give into blood magic.