The Area Design team took a look at the saves and noticed that they all had reasons that would trigger Pallegina to leave the party. Most of the companions have triggers that can cause them to leave the party if they are unhappy with decisions being made by the watcher. I'll list Pallegina's triggers below.
I do believe there was a bug where Pallegina was not leaving the party properly earlier in Deadfire's release, but the bug was fixed and allows her to leave the party as intended.
If you think you are not triggering any of these situations, we are more than happy to take a look at the conditionals set in your saves(send it to me at firstname.lastname@example.org), but so far the devs have seen that the conditionals of the saves have been triggered negatively by one of the above reasons.
Thanks everyone, and sorry for any confusion with Pallegina.
Ouch, this is very disappointing
I've been holding off sailing to the final island until now because I wanted to do everything (including the 3 dlcs) first before getting an ending. I always try to do a completionist run for my first playthrough. I was happy with my playthrough since I had max relations with everyone (except for Aloth) and did not openly antagonize any major faction in the process. I did not side with any faction, just planned to go at it solo.
Then, all of a sudden, Pallegina leaves the party without any prompting whatsoever and goes to stand in the ocean. I thought this was surely a bug since I had max relations with her and good relations with VTC as well. Also, she was standing in the ocean. Obviously, I couldn't continue playing until this got sorted out - otherwise, I'd have to just abandon one of my companions that I'd adventured with the entire game. It just breaks immersion in a big way since I'm emotionally invested in seeing *my* version of the story to the conclusion.
If Pallegina left right after one of the triggers mentioned here it might have been easier to accept. Pallegina leaving not in reaction to something I've done in-game but just because I've updated the game... this really ruins my enjoyment I don't want to come off as being too whiny, but I just wanted to describe how I feel about this issue because I love the Pillars series - to the point that I can readily forgive minor bugs and be content to wait for a patch to fix them until I start playing again.
Is there something I can do to keep Pallegina from leaving? Maybe a console command, or editing some lines in files? Even if Pallegina leaving right before endgame is indeed intended and not a bug, I would very much appreciate some way I could keep her around for the final mission...
Thank you for reading, and sorry for rambling.