I’m thinking, 17/18 year old Killian has just completed his military training and has joined the crew of the ship that’s captained by his father. One night, some mutinous crew members kill the Captain and toss him overboard. The next day, they tell Killian some story about how his father was a wanted man and he fled in the night, (they’ll have set one of the rowboats adrift during the night as proof). The guys who killed the Captain will be working with pirates, who attack once Captain Liam is out of the way. Killian is taken prisoner, and eventually comes to be a pirate, and then Captain, Dread Pirate Roberts style. If his father goes overboard, assumed dead, but maybe he’s not really dead, just mostly, that could still leave room for him to have been saved in some dark magic way that turned him into Davy Jones.
Interesting theory. I like it.