So at the end of Act 1 after you defeat Alexandar you will find him in a coma in a holding cell on the Lady Vengeance, right? How in the world does he escape from there?
I get that he's a Godwoken that keeps getting revived by Rhalic, I'm not wondering why he refuses to die. I'm wondering how he escapes from the holding cell on the Lady Vengeance without any of the characters ever being like "guys, this really important dude that were in our custody has simply vanished". I must have missed the part where this is explained, right? Otherwise it seems like a really major omission in story continuity on the developers' part.

Didn't he disappear after the ship was taken to the hall of echoes?
Maybe Dallis had someone grab him downstairs while you were fighting Dallis above decks.

My headcannon is: As he is still wearing a source collar, he couldn't "phase" with the ship as it went to the hall of echos, this kills all potential party members you didn't choose to bring, but as he was already Godwoken, rather than a potential, he is saved, possibly ending up in the ocean to be picked up by Dallis

My apologies for not responding sooner, I totally forgot I had even started this thread!

He did indeed disappear somehow when the Lady Vengeance entered the Hall of Echoes, it is briefly mentioned by someone at the very end of act 3, I believe.
I still think it's incredibly weird that nobody seems to give a damn that a major character just ups and vanishes. It's not mentioned, not talked about, not pointed to, nothing, until that brief mention much later in the game.

Sometimes, things like that are intentionally left vague - especially when it would be hard to explain - but, I agree that this should have been better fleshed out.