Hmmm. Colin has hinted that his portrayal of a pirate is more “Princess Bride” than anything else. In that movie, Westley’s ship was attacked, but rather than be killed, he’s taken captive until one day, the Dread Pirate Roberts appoints Westley to take his place as the next captain. I could imagine a similar story happening to Killian Jones.
Another possibility is that his dad was a sea captain who abandoned Killian, and Killian was found and taken aboard a pirate ship. Young Killian found a de facto family amongst the crew and rose through the ranks to become a pirate.
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"That’s how you know you’ve really got a home. When you leave it, there’s this feeling that you can’t shake. You just miss it." Neal Cassidy