I haven’t seen this theory anywhere — so here’s my two cents.
People have been guessing on the relationship between Bae and Hook. Well, after Milah’s death, Hook went to Neverland to give him time to figure out a way to kill the Dark One.
Somehow he stumbled upon Bae and found out who he was. I think he imprisoned Bae on his ship in order to manipulate Bae into telling him how to kill Rumple. Perhaps it took a long time — centuries — for Bae to finally reveal something about the dagger.
Remember, Hook returned to the Enchanted Forest centuries later (when Regina was the Queen and close to enacting the curse and had Bell locked up in the tower) and he already knew all about the dagger. He just didn’t know where to find it.
So I think Bae was a prisoner on board Hook’s ship in Neverland…perhaps he eventually became part of the crew. I doubt Hook treated him poorly for the sake of Milah, but at the same time did not want him to escape for the sake of killing Rumple. That’s how Bae learned how to sail the ship.
What do you guys think?